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galaxy-dist commit 7698203440de: Fix functional tests as they think dynamically created jQuery elements are real
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1286227378 14400 # Node ID 7698203440dec7457f6fd273a36f30ed89e05821 # Parent 8f2e21b079864cb02b2c4e5bfc3343cbf867e259 Fix functional tests as they think dynamically created jQuery elements are real --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -23,8 +23,8 @@ from galaxy.util.expressions import Expr var file_name = $(this).attr("name"); file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); // create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = $('<input type="hidden" />'); - new_file_input.attr( { "value": file_value, "name": file_name } ); + var new_file_input = $(document.createElement('input')); + new_file_input.attr( { "type", "hidden", "value": file_value, "name": file_name } ); file.after(new_file_input); } });

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galaxy-dist commit 642edc1ae4f5: Fix grid link/label bug introduced in 4372:269c46003857
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286376177 14400 # Node ID 642edc1ae4f50a0a7e6d00904654733f4172fbf7 # Parent 41cf53bdcca21a255c94ae90d20a9bd492cf6741 Fix grid link/label bug introduced in 4372:269c46003857 --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -860,13 +860,19 @@ cls = "menubutton split" %> - %if len(grid.operations) == 0: - <td><a class="label" href="${href}">${v}</a></td> - %elif href: - <td><div id="${id}" class="${cls}" style="float: left;"><a class="label" href="${href}">${v}</a></div></td> + <td> + %if href: + %if len(grid.operations) != 0: + <div id="${id}" class="${cls}" style="float: left;"> + %endif + <a class="label" href="${href}">${v}</a> + %if len(grid.operations) != 0: + </div> + %endif %else: - <td><div id="${id}" class="${cls}"><label for="${encoded_id}">${v}</label></div></td> + <div id="${id}" class="${cls}"><label for="${encoded_id}">${v}</label></div> %endif + </td> %endfor %endif %endfor

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galaxy-dist commit 8774252ac053: sample_tracking: migration script to modify the 'file_path' field type in 'sample_dataset' table to 'TEXT' so that it can support large file paths exceeding 255 characters
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1286199759 14400 # Node ID 8774252ac0531343953428a44a5a2b07e6fe514e # Parent e32d77e1f47b1fc94b3e7511094e4b0d760f1e97 sample_tracking: migration script to modify the 'file_path' field type in 'sample_dataset' table to 'TEXT' so that it can support large file paths exceeding 255 characters --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py @@ -0,0 +1,59 @@ +""" +Migration script to modify the 'file_path' field type in 'sample_dataset' table +to 'TEXT' so that it can support large file paths exceeding 255 characters +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from sqlalchemy.exc import * + +from galaxy.model.custom_types import * +from galaxy.util.json import from_json_string, to_json_string + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + + +def upgrade(): + print __doc__ + metadata.reflect() + try: + SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) + except NoSuchTableError, e: + SampleDataset_table = None + log.debug( "Failed loading table 'sample_dataset'" ) + + if SampleDataset_table: + cmd = "SELECT id, file_path FROM sample_dataset" + result = db_session.execute( cmd ) + filepath_dict = {} + for r in result: + id = int(r[0]) + filepath_dict[id] = r[1] + # remove the 'file_path' column + try: + SampleDataset_table.c.file_path.drop() + except Exception, e: + log.debug( "Deleting column 'file_path' from the 'sample_dataset' table failed: %s" % ( str( e ) ) ) + # create the column again + try: + col = Column( "file_path", TEXT ) + col.create( SampleDataset_table ) + assert col is SampleDataset_table.c.file_path + except Exception, e: + log.debug( "Creating column 'file_path' in the 'sample_dataset' table failed: %s" % ( str( e ) ) ) + + for id, file_path in filepath_dict.items(): + cmd = "update sample_dataset set file_path='%s' where id=%i" % (file_path, id) + db_session.execute( cmd ) + +def downgrade(): + pass --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -620,7 +620,7 @@ SampleDataset.table = Table('sample_data Column( "update_time", DateTime, default=now, onupdate=now ), Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), Column( "name", TrimmedString( 255 ), nullable=False ), - Column( "file_path", TrimmedString( 255 ), nullable=False ), + Column( "file_path", TEXT ), Column( "status", TrimmedString( 255 ), nullable=False ), Column( "error_msg", TEXT ), Column( "size", TrimmedString( 255 ) ) )

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galaxy-dist commit 06d6ce09e0f1: Fix for checking whether the current user can access a specified library item.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1286207081 14400 # Node ID 06d6ce09e0f152d38c632dae7ccba9337f25bab5 # Parent 8774252ac0531343953428a44a5a2b07e6fe514e Fix for checking whether the current user can access a specified library item. --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -2246,22 +2246,30 @@ class LibraryCommon( BaseController, Use message=message, status=status ) ) def _check_access( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): + can_access = True if isinstance( item, trans.model.HistoryDatasetAssociation ): - # Deny that the dataset exists if the user does not have the DATASET_ACCESS permission. - if not item or \ - not ( trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user ): - message = "Invalid history dataset id (%s) specified." % str( item.id ) - return trans.response.send_redirect( web.url_for( controller='library_common', - action='browse_library', - cntrller=cntrller, - id=library_id, - show_deleted=show_deleted, - message=util.sanitize_text( message ), - status='error' ) ) - # Deny that the item exists if the user does not have the LIBRARY_ACCESS permission on its parent library, - # or if they are not able to access the item itself. - if not item or ( not is_admin and not trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ): - message = "Invalid item id (%s) specified." % str( item.id ) + # Make sure the user has the DATASET_ACCESS permission on the history_dataset_association. + if not item: + message = "Invalid history dataset (%s) specified." % str( item ) + can_access = False + elif not trans.app.security_agent.can_access_dataset( current_user_roles, item.dataset ) and item.history.user==trans.user: + message = "You do not have permission to access the history dataset with id (%s)." % str( item.id ) + can_access = False + else: + # Make sure the user has the LIBRARY_ACCESS permission on the library item. + if not item: + message = "Invalid library item (%s) specified." % str( item ) + can_access = False + elif not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, item, trans.user ) ): + if isinstance( item, trans.model.Library ): + item_type = 'data library' + elif isinstance( item, trans.model.LibraryFolder ): + item_type = 'folder' + else: + item_type = '(unknown item type)' + message = "You do not have permission to access the %s with id (%s)." % ( item_type, str( item.id ) ) + can_access = False + if not can_access: if cntrller == 'api': return 400, message if isinstance( item, trans.model.Library ): @@ -2282,7 +2290,7 @@ class LibraryCommon( BaseController, Use def _check_add( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny access if the user is not an admin and does not have the LIBRARY_ADD permission. if not ( is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, item ) ): - message = "You are not authorized to add an item to '%s'." % item.name + message = "You are not authorized to add an item to (%s)." % item.name # Redirect to the real parent library since we know we have access to it. if cntrller == 'api': return 403, message @@ -2300,7 +2308,7 @@ class LibraryCommon( BaseController, Use if not ( is_admin or \ ( trans.app.security_agent.can_manage_library_item( current_user_roles, item ) and trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset ) ) ): - message = "You are not authorized to manage permissions on library dataset '%s'." % library_dataset.name + message = "You are not authorized to manage permissions on library dataset (%s)." % library_dataset.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2312,7 +2320,7 @@ class LibraryCommon( BaseController, Use status='error' ) ) # Deny access if the user is not an admin and does not have the LIBRARY_MANAGE permission. if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, item ) ): - message = "You are not authorized to manage permissions on '%s'." % item.name + message = "You are not authorized to manage permissions on (%s)." % item.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common', @@ -2325,7 +2333,7 @@ class LibraryCommon( BaseController, Use def _check_modify( self, trans, cntrller, is_admin, item, current_user_roles, use_panels, library_id, show_deleted ): # Deny modification if the user is not an admin and does not have the LIBRARY_MODIFY permission. if not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): - message = "You are not authorized to modify '%s'." % item.name + message = "You are not authorized to modify (%s)." % item.name if cntrller == 'api': return 403, message return trans.response.send_redirect( web.url_for( controller='library_common',

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galaxy-dist commit 51aaa9eac818: Updates to LPS tool help text.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Richard Burhans <burhans(a)bx.psu.edu> # Date 1285871526 14400 # Node ID 51aaa9eac8182b25dbbffd1de902b78c916cb0f5 # Parent ddf70ed04c8b24f9095d4b16f6041907f7c6d428 Updates to LPS tool help text. --- a/tools/human_genome_variation/lps.xml +++ b/tools/human_genome_variation/lps.xml @@ -120,7 +120,7 @@ <param name="c1" type="float" value="1e-3" help="Parameter defining the margin by which the first-order step is required to decrease before being taken."><validator type="in_range" message="0.0 < c1 < 1.0" min="0.0" max="1.0"/></param> - <param name="maxIter" type="integer" value="10000" label="Maximum number of iterations"/> + <param name="maxIter" type="integer" value="10000" label="Maximum number of iterations" help="Terminate with error if we exceed this."/><param name="stopTol" type="float" value="1e-6" label="Stop tolerance" help="Convergence tolerance for target value of lambda."/><param name="intermediateTol" type="float" value="1e-4" label="Intermediate tolerance" help="Convergence tolerance for intermediate values of lambda."/><param name="finalOnly" type="select" format="integer" label="Final only"> @@ -132,8 +132,8 @@ </inputs><outputs> - <data name="output_file" format="tabular"/> - <data name="log_file" format="txt"/> + <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: results"/> + <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log"/></outputs><requirements> @@ -188,28 +188,52 @@ There is a second output dataset (a log) **What it does** -The LASSO-Patternsearch algorithm efficiently identifies patterns of multiple -dichotomous risk factors for outcomes of interest in demographic and genomic -studies. It is designed for the case where there is a possibly very large -number of candidate patterns but it is believed that only a relatively small -number are important. +The LASSO-Patternsearch algorithm fits your dataset to an L1-regularized +logistic regression model. A benefit of using L1-regularization is +that it typically yields a weight vector with relatively few non-zero +coefficients. -If the "risky" direction (with respect to the outcome of interest) is known -for all or almost all variables, the results are readily interpretable. -If the risky direction is coded correctly for all of the variables, the -fitted model can be expected to be sparser than that for any other coding. -However, if a small number of risky variables are coded in the "wrong" way, -this usually can be detected. +For example, say you have a dataset containing M rows (subjects) +and N columns (attributes) where one of these N attributes is binary, +indicating whether or not the subject has some property of interest P. +In simple terms, LPS calculates a weight for each of the other attributes +in your dataset. This weight indicates how "relevant" that attribute +is for predicting whether or not a given subject has property P. +The L1-regularization causes most of these weights to be equal to zero, +which means LPS will find a "small" subset of the remaining N-1 attributes +in your dataset that can be used to predict P. -The input file is tabular with rows representing individuals and columns -representing variables. There is one special column, the label column, -containing +1 for cases, and -1 for controls. The other columns should be -0 or 1, with 1 representing the expected riskier value for each variable. -For instance with SNPs the column would have a 1 if the individual (row) -has the risk allele, or a 0 otherwise. The output file has one line for each -variable, or "feature" in the input file, with a single column containing the -calculated score for that feature. The log file provides information about -the input and the internal values obtained during the computation process. +In other words, LPS can be used for feature selection. + +The input dataset is tabular, and must contain a label column which +indicates whether or not a given row has property P. In the current +version of this tool, P must be encoded using +1 and -1. The Lambda_fac +parameter ranges from 0 to 1, and controls how sparse the weight +vector will be. At the low end, when Lambda_fac = 0, there will be +no regularization. At the high end, when Lambda_fac = 1, there will be +"too much" regularization, and all of the weights will equal zero. + +The LPS tool creates two output datasets. The first, called the results +file, is a tabular dataset containing one column of weights for each +value of the regularization parameter lambda that was tried. The weight +columns are in order from left to right by decreasing values of lambda. +The first N-1 rows in each column are the weights for the N-1 attributes +in your input dataset. The final row is a constant, the intercept. + +Let **x** be a row from your input dataset and let **b** be a column +from the results file. To compute the probability that row **x** has +a label value of +1: + + Probability(row **x** has label value = +1) = 1 / [1 + exp{**x** \* **b**\[1..n-1\] + **b**\[n\]}] + +where **x** \* **b**\[1..n-1\] represents matrix multiplication. + +The second output dataset, called the log file, is a text file which +contains additional data about the fitted L1-regularized logistic +regression model. These data include the number of features, the +computed value of lambda_max, the actual values of lambda used, the +optimal values of the log-likelihood and regularized log-likelihood +functions, the number of non-zeros, and the number of iterations. Website: http://pages.cs.wisc.edu/~swright/LPS/ @@ -235,11 +259,16 @@ Website: http://pages.cs.wisc.edu/~swrig - output log file:: - Data set has 100 vectors with 50 features - calculateLambdaMax: n=50, m=100, m+=50, m-=50 - computed value of lambda_max: 5.0000e-01 - lambda=2.50e-02 solution has 10 nonzeros. - It required 546 iterations + Data set has 100 vectors with 50 features. + calculateLambdaMax: n=50, m=100, m+=50, m-=50 + computed value of lambda_max: 5.0000e-01 + + lambda=2.96e-02 solution: + optimal log-likelihood function value: 6.46e-01 + optimal *regularized* log-likelihood function value: 6.79e-01 + number of nonzeros at the optimum: 5 + number of iterations required: 43 + etc. ----- --- a/test-data/lps_arrhythmia_log.txt +++ b/test-data/lps_arrhythmia_log.txt @@ -1,5 +1,4 @@ -Data set has 452 vectors with 279 features - +Data set has 452 vectors with 279 features. Sampled 452 points out of 452 calculateLambdaMax: n=279, m=452, m+=245, m-=207 computed value of lambda_max: 1.8231e+02 @@ -52,36 +51,147 @@ iter 1, gpnorm=1.7618e-09, nonzero= **** Initial point: nz=1, f= 0.689609056404, lambda= 5.469e+00 iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01 Function evals = 2, Gradient evals = 1.0 -lambda=1.64e+02 solution has 1 nonzeros. -It required 6 iterations -lambda=1.17e+02 solution has 1 nonzeros. -It required 1 iterations +lambda=1.64e+02 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 6 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=8.31e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=1.17e+02 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=5.91e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=8.31e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=4.21e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=5.91e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=3.00e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=4.21e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=2.13e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=3.00e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=1.52e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=2.13e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=1.08e+01 solution has 1 nonzeros. -It required 1 iterations +lambda=1.52e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=7.68e+00 solution has 1 nonzeros. -It required 1 iterations +lambda=1.08e+01 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. -lambda=5.47e+00 solution has 1 nonzeros. -It required 1 iterations +lambda=7.68e+00 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. +lambda=5.47e+00 solution: + optimal log-likelihood function value: 6.90e-01 + optimal *regularized* log-likelihood function value: 6.90e-01 + number of non-zeros at the optimum: 1 + number of iterations required: 1 + prediction using this solution: + 54.20% of vectors were correctly predicted. + 245 correctly predicted. + 207 in +1 predicted to be in -1. + 0 in -1 predicted to be in +1. + 0 in +1 with 50/50 chance. + 0 in -1 with 50/50 chance. +

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galaxy-dist commit ba6f40c5b3d3: Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1285964434 14400 # Node ID ba6f40c5b3d3ee82aa6719f98f58d4285bcbd66d # Parent 4990d7b95b7273ba7159bfb2db1931a4e74a980a Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates. --- a/templates/requests/common/new_request.mako +++ b/templates/requests/common/new_request.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#new_request" ).submit(); - } - }); -}); -</script> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -9,30 +9,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#registration" ).submit(); - } - }); - }); - </script></%def><% --- a/templates/library/common/folder_info.mako +++ b/templates/library/common/folder_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><% --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return fa lse};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f= g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var e=$(this);var h=e.find("option").length;if((h<a)||(h>b)){return}if(e.attr("multiple")==true){return}if(e.hasClass("no-autocomplete")){return}var l=e.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",e.attr("name"));c.attr("id",e.attr("id"));c.click(function(){var m=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(m);$(this ).select()});var f=[];var i={};e.children("option").each(function(){var n=$(this).text();var m=$(this).attr("value");f.push(n);i[n]=m;i[m]=m;if(m==l){c.attr("value",n)}});if(l==""||l=="?"){c.attr("value","Click to Search or Select")}if(e.attr("name")=="dbkey"){f=f.sort(naturalSort)}var g={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(f,g);e.replaceWith(c);var k=function(){var n=c.attr("value");var m=i[n];if(m!==null&&m!==undefined){c.attr("value",m)}else{if(l!=""){c.attr("value",l)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(e.attr("refresh_on_change")=="true"){var d=e.attr("refresh_on_change_values");if(d!==undefined){d=d.split(",")}var j=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){refresh=false;if(d!==undefined){for(var m=0;m<d.length;m++){if(n==d[m]){refresh=true;break}}}else{refres h=true}if(refresh){c.attr("value",n);c.parents("form").submit()}}};c.bind("result",j);c.keyup(function(m){if(m.keyCode===13){j()}});c.keydown(function(m){if(m.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();retur n})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state" ,k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(t his).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}function GalaxyAsync(a){this.url_dict={};this.log_action=(a===undefined?false:a)}GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset t o browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); +function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return fa lse};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f= g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this ).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window). trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}funct ion init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}retu rn false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show ()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to br owser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/library/common/library_info.mako +++ b/templates/library/common/library_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><% --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -13,43 +13,24 @@ from galaxy.util.expressions import Expr ${h.css( "base", "autocomplete_tagging" )} ${h.js( "jquery", "galaxy.base", "jquery.autocomplete" )} <script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } +$(function() { + $(window).bind("refresh_on_change", function() { + $(':file').each( function() { + var file = $(this); + var file_value = file.val(); + if (file_value) { + // disable file input, since we don't want to upload the file on refresh + var file_name = $(this).attr("name"); + file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } ); + // create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = $('<input type="hidden" />'); + new_file_input.attr( { "value": file_value, "name": file_name } ); + file.after(new_file_input); } - } - else { - refresh = true; - } - if ( refresh ){ - $( ':file' ).each( function() { - var file_value = $( this )[0].value; - if ( file_value ) { - //disable file input, since we don't want to upload the file on refresh - var file_name = $( this )[0].name; - $( this )[0].name = 'replaced_file_input_' + file_name - $( this )[0].disable = true; - //create a new hidden field which stores the filename and has the original name of the file input - var new_file_input = document.createElement( 'input' ); - new_file_input.type = 'hidden'; - new_file_input.value = file_value; - new_file_input.name = file_name; - document.getElementById( 'tool_form' ).appendChild( new_file_input ); - } - } ); - $( "#tool_form" ).submit(); - } - }); + }); + }); }); + %if not add_frame.debug: if( window.name != "galaxy_main" ) { location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' ); --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#find_request" ).submit(); - } - }); -}); -</script> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -119,7 +119,7 @@ function make_popup_menus() { } // Alphanumeric/natural sort fn -function naturalSort(a, b){ +function naturalSort(a, b) { // setup temp-scope variables for comparison evauluation var re = /(-?[0-9\.]+)/g, x = a.toString().toLowerCase() || '', @@ -249,45 +249,24 @@ function replace_big_select_inputs(min_l $(document).bind("convert_dbkeys", function() { submit_hook(); } ); // If select is refresh on change, mirror this behavior. - if (select_elt.attr('refresh_on_change') == 'true') - { + if (select_elt.attr('refresh_on_change') == 'true') { // Get refresh vals. - var refresh_vals = select_elt.attr('refresh_on_change_values'); - if (refresh_vals !== undefined) - refresh_vals = refresh_vals.split(","); - + var ref_on_change_vals = select_elt.attr('refresh_on_change_values'), + last_selected_value = select_elt.attr("last_selected_value"); + if (ref_on_change_vals !== undefined) + ref_on_change_vals = ref_on_change_vals.split(','); + // Function that attempts to refresh based on the value in the text element. - var try_refresh_fn = function() - { - // - // If value entered can be matched to value, do so and refresh by submitting parent form. - // - + var try_refresh_fn = function() { // Get new value and see if it can be matched. - var cur_value = text_input_elt.attr('value'); - var new_value = select_mapping[cur_value]; - if (new_value !== null && new_value !== undefined) - { - // Do refresh if new value is refresh value or if there are no refresh values. - refresh = false; - if (refresh_vals !== undefined) - { - for (var i= 0; i < refresh_vals.length; i++ ) - if (new_value == refresh_vals[i]) - { - refresh = true; - break; - } + var new_value = select_mapping[text_input_elt.attr('value')]; + if (new_value !== null && new_value !== undefined) { + if ($.inArray(new_value, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; } - else - // Refresh for all values. - refresh = true; - - if (refresh) - { - text_input_elt.attr('value', new_value); - text_input_elt.parents('form').submit(); - } + text_input_elt.attr('value', new_value); + $(window).trigger("refresh_on_change"); + text_input_elt.parents('form').submit(); } }; @@ -295,15 +274,17 @@ function replace_big_select_inputs(min_l // case a user may have manually entered a value that needs to be refreshed). text_input_elt.bind("result", try_refresh_fn); text_input_elt.keyup( function(e) { - if ( e.keyCode === 13 ) // Return key + if (e.keyCode === 13) { // Return key try_refresh_fn(); + } }); - // Disable return key so that it does not submit the form automatically. This is done because elememnt should behave like a + // Disable return key so that it does not submit the form automatically. This is done because element should behave like a // select (enter = select), not text input (enter = submit form). text_input_elt.keydown( function(e) { - if ( e.keyCode === 13 ) // Return key + if (e.keyCode === 13) { // Return key return false; + } }); } }); @@ -482,13 +463,13 @@ function commatize( number ) { } // Reset tool search to start state. -function reset_tool_search( initValue ) -{ +function reset_tool_search( initValue ) { // Function may be called in top frame or in tool_menu_frame; // in either case, get the tool menu frame. var tool_menu_frame = $("#galaxy_tools").contents(); - if (tool_menu_frame.length == 0) + if (tool_menu_frame.length == 0) { tool_menu_frame = $(document); + } // Remove classes that indicate searching is active. $(this).removeClass("search_active"); @@ -499,18 +480,18 @@ function reset_tool_search( initValue ) tool_menu_frame.find(".toolTitle").show(); tool_menu_frame.find(".toolPanelLabel").show(); tool_menu_frame.find(".toolSectionWrapper").each( function() { - if ($(this).attr('id') != 'recently_used_wrapper') + if ($(this).attr('id') != 'recently_used_wrapper') { // Default action. $(this).show(); - else if ($(this).hasClass("user_pref_visible")) + } else if ($(this).hasClass("user_pref_visible")) { $(this).show(); + } }); tool_menu_frame.find("#search-no-results").hide(); // Reset search input. tool_menu_frame.find("#search-spinner").hide(); - if (initValue) - { + if (initValue) { var search_input = tool_menu_frame.find("#tool-search-query"); search_input.val("search tools"); search_input.css("font-style", "italic"); @@ -518,20 +499,17 @@ function reset_tool_search( initValue ) } // Create GalaxyAsync object. -function GalaxyAsync(log_action) -{ +var GalaxyAsync = function(log_action) { this.url_dict = {}; this.log_action = (log_action === undefined ? false : log_action); } -GalaxyAsync.prototype.set_func_url = function( func_name, url ) -{ - this.url_dict[func_name] = url; +GalaxyAsync.prototype.set_func_url = function( func_name, url ) { + this.url_dict[func_name] = url; }; // Set user preference asynchronously. -GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) -{ +GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) { // Get URL. var url = this.url_dict[arguments.callee]; if (url === undefined) { return false; } @@ -544,8 +522,7 @@ GalaxyAsync.prototype.set_user_pref = fu }; // Log user action asynchronously. -GalaxyAsync.prototype.log_user_action = function( action, context, params ) -{ +GalaxyAsync.prototype.log_user_action = function( action, context, params ) { if (!this.log_action) { return; } // Get URL. @@ -588,7 +565,24 @@ GalaxyAsync.prototype.log_user_action = }); + $(document).ready( function() { + $("select[refresh_on_change='true']").change( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/templates/requests/common/edit_request.mako +++ b/templates/requests/common/edit_request.mako @@ -5,31 +5,6 @@ ${render_msg( message, status )} %endif -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_request" ).submit(); - } - }); -}); -</script> - <br/><br/><ul class="manage-table-actions"> --- a/templates/webapps/galaxy/user/info.mako +++ b/templates/webapps/galaxy/user/info.mako @@ -2,31 +2,6 @@ <%namespace file="/user/info.mako" import="render_user_info" /><%namespace file="/message.mako" import="render_msg" /> -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#user_info" ).submit(); - } - }); -}); -</script> - %if message: ${render_msg( message, status )} %endif --- a/templates/admin/forms/edit_form.mako +++ b/templates/admin/forms/edit_form.mako @@ -6,31 +6,6 @@ %endif <script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_form" ).submit(); - } - }); -}); -</script> - -<script type="text/javascript"> $(document).ready(function(){ //hide the all of the element with class msg_body $(".msg_body").hide(); --- a/templates/library/common/upload.mako +++ b/templates/library/common/upload.mako @@ -14,31 +14,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#upload_library_dataset" ).submit(); - } - }); - }); - </script></%def><%def name="stylesheets()"> --- a/templates/library/common/ldda_edit_info.mako +++ b/templates/library/common/ldda_edit_info.mako @@ -6,30 +6,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def><%def name="stylesheets()"> --- a/templates/library/common/library_dataset_info.mako +++ b/templates/library/common/library_dataset_info.mako @@ -4,30 +4,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def> %if library_dataset == library_dataset.library_dataset_dataset_association.library_dataset: --- a/templates/requests/common/show_request.mako +++ b/templates/requests/common/show_request.mako @@ -19,29 +19,6 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#show_request" ).submit(); - } - }); - }); - function showContent(vThis) { // http://www.javascriptjunkie.com --- a/templates/library/common/select_template.mako +++ b/templates/library/common/select_template.mako @@ -5,30 +5,6 @@ from galaxy.web.form_builder import CheckboxField inheritable_check_box = CheckboxField( 'inheritable' ) %> -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#select_template" ).submit(); - } - }); -}); -</script><br/><br/><ul class="manage-table-actions"> --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -25,30 +25,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - var refresh = false; - var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) - if ( refresh_on_change_values ) { - refresh_on_change_values = refresh_on_change_values.value.split( ',' ); - var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); - for( i= 0; i < refresh_on_change_values.length; i++ ) { - if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ - refresh = true; - break; - } - } - } - else { - refresh = true; - } - if ( refresh ){ - $( "#edit_info" ).submit(); - } - }); - }); - </script></%def> %if current_version:

1 0

galaxy-dist commit 7b431b0dbc68: Fixed broken indentation.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Richard Burhans <burhans(a)bx.psu.edu> # Date 1285872631 14400 # Node ID 7b431b0dbc687c1496ef5fba92dd443476d61d60 # Parent 51aaa9eac8182b25dbbffd1de902b78c916cb0f5 Fixed broken indentation. --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -646,10 +646,10 @@ class TwillTestCase( unittest.TestCase ) s2 = os.path.getsize(local_name) if abs(s1-s2) > int(delta): raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) - else: - raise Exception, 'Unimplemented Compare type: %s' % compare - if extra_files: - self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare + if extra_files: + self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) except AssertionError, err: errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) errmsg += str( err )

1 0

galaxy-dist commit 4990d7b95b72: Bug fix for signature of lib.galaxy_utils.sequence.transform.?NA_reverse_complement method.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1285944317 14400 # Node ID 4990d7b95b7273ba7159bfb2db1931a4e74a980a # Parent 7b431b0dbc687c1496ef5fba92dd443476d61d60 Bug fix for signature of lib.galaxy_utils.sequence.transform.?NA_reverse_complement method. --- a/lib/galaxy_utils/sequence/transform.py +++ b/lib/galaxy_utils/sequence/transform.py @@ -19,10 +19,10 @@ def DNA_complement( sequence ): def RNA_complement( sequence ): return sequence.translate( RNA_COMPLEMENT ) #returns the reverse complement of the sequence -def DNA_reverse_complement( self, sequence ): +def DNA_reverse_complement( sequence ): sequence = reverse( sequence ) return DNA_complement( sequence ) -def RNA_reverse_complement( self, sequence ): +def RNA_reverse_complement( sequence ): sequence = reverse( sequence ) return RNA_complement( sequence ) def to_DNA( sequence ):

1 0

galaxy-dist commit e32d77e1f47b: Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1286147560 14400 # Node ID e32d77e1f47b1fc94b3e7511094e4b0d760f1e97 # Parent ba6f40c5b3d3ee82aa6719f98f58d4285bcbd66d Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base. --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -241,8 +241,7 @@ <% user = association.user %><tr><td> - ${user.email} - <a id="user-${i}-popup" class="popup-arrow" style="display: none;">▼</a> + <div class="menubutton popup" id="user-${i}-popup">${user.email}</div></td><td><div popupmenu="user-${i}-popup"> --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return fa lse};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f= g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this).val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this ).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window). trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}funct ion init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}retu rn false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show ()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to br owser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); +function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return fa lse};$(b).bind("click",c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");if(obj_length(b)<=0){$("<li/>").html("No options").appendTo(a)}$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));a.find("a").bind("click",function(b){b.stopPropagation();return true});make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}funct ion naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString().toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).split(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a,b){if(!jQuery().autocomplete){return}if(a===undefined){a=20}if(b===undefined){b=3000}$("select").each(function(){var d=$(this);var g=d.find("option").length;if((g<a)||(g>b)){return}if(d.attr("multiple")==true){return}if(d.hasClass("no-autocomplete")){return}var m=d.attr("value");var c=$("<input type='text' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",d.attr("name"));c.attr("id",d.attr("id"));c.click(function(){var n=$(this). val();$(this).val("Loading...");$(this).showAllInCache();$(this).val(n);$(this).select()});var e=[];var i={};d.children("option").each(function(){var o=$(this).text();var n=$(this).attr("value");e.push(o);i[o]=n;i[n]=n;if(n==m){c.attr("value",o)}});if(m==""||m=="?"){c.attr("value","Click to Search or Select")}if(d.attr("name")=="dbkey"){e=e.sort(naturalSort)}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!=""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_dbkeys",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(n!==null&&n!==undefined){if ($.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}} )}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");i f(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrappe r"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data- url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")},Cancel:function(){d.hide_modal()}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -50,7 +50,7 @@ <%def name="grid_javascripts()"><script type="text/javascript"> - $( document ).ready( function () { + $(function () { $("#library-grid").each( function() { // Recursively fill in children and descendents of each row var process_row = function( q, parents ) { @@ -70,7 +70,7 @@ // remembering folder states, we'll need something // more sophisticated here. var visible = false; - $(q).find( "span.expandLink").click( function() { + var expand_fn = function() { if ( visible ) { descendents.hide(); descendents.removeClass( "expanded" ); @@ -81,7 +81,9 @@ q.addClass( "expanded" ); visible = true; } - }); + }; + $(q).find("span.expandLink").click(expand_fn); + $(q).find("span.expandLink a").click(expand_fn); // Check/uncheck boxes in subfolders. q.children( "td" ).children( "input[type=checkbox]" ).click( function() { if ( $(this).is(":checked") ) { @@ -103,6 +105,17 @@ }); }); }); + + // For view info links, use a modal popup + /*$(".view-info").live("click", function() { + $.get( $(this).attr("href"), function(info) { + show_modal("View Information", info, { + "Close": function() { hide_modal(); } + }); + }); + return false; + });*/ + function checkForm() { if ( $("select#action_on_datasets_select option:selected").text() == "delete" ) { if ( confirm( "Click OK to delete these datasets?" ) ) { @@ -198,55 +211,56 @@ %endif id="libraryItem-${ldda.id}"><td style="padding-left: ${pad+20}px;"> + <input style="float: left;" type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}" %if selected: - <input type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}" checked/> - %else: - <input type="checkbox" name="ldda_ids" value="${trans.security.encode_id( ldda.id )}"/> + checked="checked" %endif + /> %if ldda.library_dataset.deleted: <span class="libraryItem-error"> - %endif - <a href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name[:50]}</a> - %if ldda.library_dataset.deleted: - </span> - %endif - %if not library.deleted: - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: - %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): - <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> - %endif - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> - %endif - %if can_modify: - %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> - %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: - <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> - %endif - %endif - </div> - %endif + %endif + <div style="float: left; margin-left: 1px;" class="menubutton split popup" id="dataset-${ldda.id}-popup"> + <a class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">${ldda.name[:50]}</a> + </div> + %if ldda.library_dataset.deleted: + </span> + %endif + %if not library.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %else: + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and not info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify and info_association: + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_manage: + %if not trans.app.security_agent.dataset_is_public( ldda.dataset ): + <a class="action-button" href="${h.url_for( controller='library_common', action='make_library_item_public', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_type='ldda', id=trans.security.encode_id( ldda.dataset.id ), use_panels=use_panels, show_deleted=show_deleted )}">Make public</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and can_modify: + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if can_modify: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_common', action='delete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif </td><td id="libraryItemInfo">${render_library_item_info( ldda )}</td><td>${uploaded_by}</td> @@ -266,12 +280,12 @@ if root_folder: pad = folder_pad - expander = "/static/images/silk/resultset_bottom.png" - folder_img = "/static/images/silk/folder_page.png" + expander = h.url_for("/static/images/silk/resultset_bottom.png") + folder_img = h.url_for("/static/images/silk/folder_page.png") else: pad = folder_pad + 20 - expander = "/static/images/silk/resultset_next.png" - folder_img = "/static/images/silk/folder.png" + expander = h.url_for("/static/images/silk/resultset_next.png") + folder_img = h.url_for("/static/images/silk/folder.png") if created_ldda_ids: created_ldda_ids = util.listify( created_ldda_ids ) if str( folder.id ) in hidden_folder_ids: @@ -311,14 +325,16 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <span class="expandLink"><span class="rowIcon"></span><a style="margin-left: 5px;" href="javascript:void(0);">${folder.name}</a></span> + <span class="expandLink"><span class="rowIcon"></span> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="folder_img-${folder.id}-popup"> + <a href="javascript:void(0);">${folder.name}</a> + </div> %if folder.deleted: </span> %endif %if not branch_deleted( folder ): %if not library.deleted: - <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="folder_img-${folder.id}-popup"> %if not branch_deleted( folder ) and can_add: <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> @@ -328,7 +344,7 @@ %if can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> + <a class="action-button" class="view-info" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif %endif %if not branch_deleted( folder ) and can_modify and not info_association: --- a/static/june_2007_style/blue/library.css +++ b/static/june_2007_style/blue/library.css @@ -13,7 +13,7 @@ pre.peek{background:white;color:black;wi pre.peek th{color:white;background:#023858;} span.expandLink{padding-left:20px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat;} .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat;} -.folderRow span.rowIcon{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} +.folderRow span.rowIcon{float:left;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} .libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AA6666;background:#FFCCCC;} .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #888888;background:#EEEEEE;} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AAAA66;background:#FFFFCC;} --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -43,7 +43,7 @@ function attach_popupmenu( button_elemen $("#popup-helper").unbind( "click.popupmenu" ).hide(); // $(document).unbind( "click.popupmenu" ); }; - var click = function( e ) { + var click_handler = function( e ) { // var o = $(button_element).offset(); $("#popup-helper").bind( "click.popupmenu", clean ).show(); // $(document).bind( "click.popupmenu", clean ); @@ -62,7 +62,7 @@ function attach_popupmenu( button_elemen } ); return false; }; - $( button_element ).click( click ); + $(button_element).bind("click", click_handler); } function make_popupmenu( button_element, options ) { @@ -112,6 +112,10 @@ function make_popup_menus() { }; }); var b = $( "#" + $(this).attr( 'popupmenu' ) ); + b.find("a").bind("click", function(e) { + e.stopPropagation(); // Stop bubbling so clicking on the link goes through + return true; + }); make_popupmenu( b, options ); $(this).remove(); b.addClass( "popup" ).show(); --- a/static/june_2007_style/library.css.tmpl +++ b/static/june_2007_style/library.css.tmpl @@ -76,6 +76,7 @@ span.expandLink { } .folderRow span.rowIcon { + float: left; width: 16px; height: 16px; display: inline-block; --- a/templates/library/common/library_info.mako +++ b/templates/library/common/library_info.mako @@ -34,9 +34,10 @@ <div class="toolForm"><div class="toolFormTitle"> - <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}"><b>${library.name[:50]}</b></a> + <div class="menubutton split popup" id="library-${library.id}-popup"> + <a href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">${library.name[:50]}</a> + </div> %if can_add or can_modify or can_manage: - <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="library-${library.id}-popup"> %if not library.deleted: %if can_add and not library.info_association: --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -46,9 +46,8 @@ <div class="toolForm"><div class="toolFormTitle"> - Information about ${ldda.name} + Information about <div class="menubutton popup" id="dataset-${ldda.id}-popup">${ldda.name}</div> %if not library.deleted and not branch_deleted( ldda.library_dataset.folder ) and not ldda.library_dataset.deleted: - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a><div popupmenu="dataset-${ldda.id}-popup"> %if can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>

1 0

galaxy-dist commit 8f2e21b07986: Enable export history jobs to work when application option 'outputs_to_working_directory' is set to true. This will enable export history jobs to work on galaxy main and, more generally, when galaxy datasets are mounted read-only.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286208862 14400 # Node ID 8f2e21b079864cb02b2c4e5bfc3343cbf867e259 # Parent 06d6ce09e0f152d38c632dae7ccba9337f25bab5 Enable export history jobs to work when application option 'outputs_to_working_directory' is set to true. This will enable export history jobs to work on galaxy main and, more generally, when galaxy datasets are mounted read-only. --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -321,6 +321,20 @@ class JobWrapper( object ): inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] ) + + # Set up output dataset association for export history jobs. Because job + # uses a Dataset rather than an HDA or LDA, it's necessary to set up a + # fake dataset association that provides the needed attributes for + # preparing a job. + class FakeDatasetAssociation ( object ): + def __init__( self, dataset=None ): + self.dataset = dataset + self.file_name = dataset.file_name + self.metadata = dict() + self.children = [] + jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first() + if jeha: + out_data[ "output_file" ] = FakeDatasetAssociation( dataset=jeha.dataset ) # These can be passed on the command line if wanted as $userId $userEmail if job.history and job.history.user: # check for anonymous user! userId = '%d' % job.history.user.id @@ -632,13 +646,21 @@ class JobWrapper( object ): return self.false_path job = self.sa_session.query( model.Job ).get( self.job_id ) + # Job output datasets are combination of output datasets, library datasets, and jeha datasets. + jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first() if self.app.config.outputs_to_working_directory: self.output_paths = [] for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) self.output_paths.append( DatasetPath( data.id, data.file_name, false_path ) ) + if jeha: + false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) ) + self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name, false_path ) ) else: self.output_paths = [ DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) for da in job.output_datasets + job.output_library_datasets ] + if jeha: + self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name ) ) + return self.output_paths def get_output_file_id( self, file ): --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -15,12 +15,15 @@ def load_history_imp_exp_tools( toolbox <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history"><type class="ExportHistoryTool" module="galaxy.tools"/><action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/> - <command>$__SET_EXPORT_HISTORY_COMMAND_LINE__</command> + <command>$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command><inputs><param name="__HISTORY_TO_EXPORT__" type="hidden"/><param name="compress" type="boolean"/> - <param name="__SET_EXPORT_HISTORY_COMMAND_LINE__" type="hidden"/> + <param name="__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__" type="hidden"/></inputs> + <outputs> + <data format="gzip" name="output_file"/> + </outputs></tool> """ tmp_name = tempfile.NamedTemporaryFile() @@ -40,7 +43,9 @@ class JobExportHistoryArchiveWrapper( ob # jeha = job_export_history_archive for the job. """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha - object, and returns a command line for running the job. """ + object, and returns a command line for running the job. The command line + includes the command, inputs, and options; it does not include the output + file because it must be set at runtime. """ # # Helper methods/classes. @@ -199,10 +204,9 @@ class JobExportHistoryArchiveWrapper( ob options = "" if jeha.compressed: options = "-G" - return "python %s %s %s %s %s %s" % ( + return "python %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \ - options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename, \ - jeha.dataset.file_name ) + options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename ) def cleanup_after_job( self, db_session ): """ Remove temporary directory and attribute files generated during setup for this job. """ --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -61,7 +61,7 @@ class ExportHistoryToolAction( ToolActio # Set additional parameters. incoming[ '__HISTORY_TO_EXPORT__' ] = history.id - incoming[ '__SET_EXPORT_HISTORY_COMMAND_LINE__' ] = cmd_line + incoming[ '__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' ] = cmd_line for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value )

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galaxy-dist commit 546dc4845175: New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1285818943 14400 # Node ID 546dc4845175c92c91e181af61b6e1d2a108230e # Parent 940d77bec4d59a5418f9f731ca6ca114d748aa5d New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test. --- /dev/null +++ b/test-data/wig_to_bigwig_hg17.len @@ -0,0 +1,46 @@ +chr10 135413628 +chr10_random 113275 +chr11 134452384 +chr12 132449811 +chr12_random 466818 +chr13 114142980 +chr13_random 186858 +chr14 106368585 +chr15 100338915 +chr15_random 784346 +chr16 88827254 +chr16_random 105485 +chr17 78774742 +chr17_random 2618010 +chr18 76117153 +chr18_random 4262 +chr19 63811651 +chr19_random 301858 +chr1 245522847 +chr1_random 3897131 +chr20 62435964 +chr21 46944323 +chr22 49554710 +chr22_random 257318 +chr2 243018229 +chr2_random 418158 +chr3 199505740 +chr3_random 970716 +chr4 191411218 +chr4_random 1030282 +chr5 180857866 +chr5_random 143687 +chr6 170975699 +chr6_random 1875562 +chr6_hla_hap1 139182 +chr6_hla_hap2 150447 +chr7 158628139 +chr7_random 778964 +chr8 146274826 +chr8_random 943810 +chr9 138429268 +chr9_random 1312665 +chrM 16571 +chrX 154824264 +chrX_random 1719168 +chrY 57701691 Binary file test-data/nj_tree_pdf_out.pdf has changed --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -108,4 +108,10 @@ for dir in $DIRS; do fi done +# for wig_to_bigWig +if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then + mkdir -p tool-data/shared/ucsc/chrom + cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len +fi + python ./scripts/fetch_eggs.py all

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galaxy-dist commit 8729d2e29b02: removed unused mako template
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290029052 18000 # Node ID 8729d2e29b02be031448abff34d5587b5d0d94c3 # Parent c4441790bfaae82d4e84ad11ec58cea7715ea6ef removed unused mako template --- a/templates/admin/requests/edit_request_type.mako +++ /dev/null @@ -1,79 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - - -%if message: - ${render_msg( message, status )} -%endif - -<% num_states=len(states_list) %> - -<div class="toolForm"> - <div class="toolFormTitle">Edit the sequencer configuration</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='request_type', save_changes=True, create=False, id=request_type.id, num_states=num_states )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${request_type.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="description" value="${request_type.desc}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label> - Sequencing request form definition: - </label> - <select name="form_id"> - %for form in forms: - %if form.id == request_type.request_form_id: - <option value="${form.id}" selected>${form.name}</option> - %else: - <option value="${form.id}">${form.name}</option> - %endif - %endfor - </select> - </div> - <div class="form-row"> - <label> - Sample form definition: - </label> - <select name="form_id"> - %for form in forms: - %if form.id == request_type.sample_form_id: - <option value="${form.id}" selected>${form.name}</option> - %else: - <option value="${form.id}">${form.name}</option> - %endif - %endfor - </select> - </div> - <div class="toolFormBody"> - %for element_count, state in enumerate(states_list): - <div class="form-row"> - <label>${1+element_count}) State name:</label> - <input type="text" name="new_element_name_${element_count}" value="${state.name}" size="40"/> - <label>State help text (optional):</label> - <input type="text" name="new_element_description_${element_count}" value="${state.desc}" size="40"/> - </div> - <div style="clear: both"></div> - %endfor - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="new" value="submitted" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="edit_request_type_button" value="Save"/> - </div> - </form> - </div> -</div>

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galaxy-dist commit ddf70ed04c8b: sff_extractor tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1285855763 14400 # Node ID ddf70ed04c8b24f9095d4b16f6041907f7c6d428 # Parent 546dc4845175c92c91e181af61b6e1d2a108230e sff_extractor tool output is now explicitly set to fastqsanger when the fastq option is selected. patch by peter(a)maubp.freeserve.co.uk --- a/tools/filters/sff_extractor.xml +++ b/tools/filters/sff_extractor.xml @@ -14,7 +14,7 @@ <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" /></inputs><outputs> - <data format="fastq" name="out_file1" > + <data format="fastqsanger" name="out_file1" ><filter>fastq_output is True</filter></data><data format="xml" name="out_file2">

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galaxy-dist commit c4441790bfaa: Fixed naming of the library selectfield for sample operations
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290028751 18000 # Node ID c4441790bfaae82d4e84ad11ec58cea7715ea6ef # Parent 29227c9c599292f7608e61cdd4b2be424b7a7bfc Fixed naming of the library selectfield for sample operations Fixed the broken popup menu in the data transfer grid Fixed the missing required/optional field info in the request form --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1584,7 +1584,7 @@ class FormDefinition( object ): if field[ 'helptext' ]: helptext='%s (%s)' % ( field[ 'helptext' ], req ) else: - helptext = '' + helptext = '(%s)' % req widgets.append( dict( label=field[ 'label' ], widget=field_widget, helptext=helptext ) ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -185,7 +185,7 @@ class RequestsCommon( BaseController, Us if request_type is not None or status == 'error': # Either the user selected a request_type or an error exists on the form. if is_admin: - if not user_id_encoded: + if not user_id_encoded and user: selected_user_id = trans.security.encode_id( user.id ) else: selected_user_id = user_id @@ -465,7 +465,7 @@ class RequestsCommon( BaseController, Us sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, request.user, - 0, + 'sample_operation', libraries, None, **kwd ) @@ -810,7 +810,6 @@ class RequestsCommon( BaseController, Us # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) for index in range( num_samples_to_add ): - id_index = len( displayable_sample_widgets ) + 1 if copy_sample_index != -1: # The user has selected a sample to copy. library_id = displayable_sample_widgets[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) @@ -826,7 +825,7 @@ class RequestsCommon( BaseController, Us # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, user=request.user, - sample_index=id_index, + sample_index=len( displayable_sample_widgets ), libraries=libraries, sample=None, library_id=library_id, @@ -1080,13 +1079,8 @@ class RequestsCommon( BaseController, Us action='update_request_state', request_id=trans.security.encode_id( request.id ) ) ) elif sample_operation == trans.model.Sample.bulk_operations.SELECT_LIBRARY: - # TODO: fix the code so that the sample_operation_select_field does not use - # sample_0_library_id as it's name. it should use something like sample_operation_library_id - # and sample_operation_folder_id because the name sample_0_library_id should belong to the - # first sample since all other form field values are named like this. The library and folder - # are skewed to be named +1 resulting in the forced use of id_index everywhere... - library_id = params.get( 'sample_0_library_id', 'none' ) - folder_id = params.get( 'sample_0_folder_id', 'none' ) + library_id = params.get( 'sample_operation_library_id', 'none' ) + folder_id = params.get( 'sample_operation_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] @@ -1254,15 +1248,14 @@ class RequestsCommon( BaseController, Us if sample_operation != 'none': # The sample_operatin param has a value other than 'none', and a specified # set of samples was received. - library_id = util.restore_text( params.get( 'sample_0_library_id', 'none' ) ) - folder_id = util.restore_text( params.get( 'sample_0_folder_id', 'none' ) ) + library_id = util.restore_text( params.get( 'sample_operation_library_id', 'none' ) ) + folder_id = util.restore_text( params.get( 'sample_operation_folder_id', 'none' ) ) # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): - id_index = index + 1 if sample is None: # Use the sample from the request object since it will not have updated values from kwd. sample = request.samples[ index ] @@ -1277,10 +1270,10 @@ class RequestsCommon( BaseController, Us sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, sample.bar_code ) ) - library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) + library_id = util.restore_text( params.get( 'sample_%i_library_id' % index, '' ) ) if not library_id and sample.library: library_id = trans.security.encode_id( sample.library.id ) - folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) + folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % index, '' ) ) if not folder_id and sample.folder: folder_id = trans.security.encode_id( sample.folder.id ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) @@ -1290,7 +1283,7 @@ class RequestsCommon( BaseController, Us field_values.append( field_value ) library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, - sample_index=id_index, + sample_index=index, libraries=libraries, sample=sample, library_id=library_id, @@ -1311,17 +1304,16 @@ class RequestsCommon( BaseController, Us name = util.restore_text( params.get( 'sample_%i_name' % index, '' ) ) if not name: break - id_index = index + 1 bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, '' ) ) - library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) - folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) + library_id = util.restore_text( params.get( 'sample_%i_library_id' % index, '' ) ) + folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % index, '' ) ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) field_values = [] for field_index in range( len( request.type.sample_form.fields ) ): field_values.append( util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) ) library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, - sample_index=id_index, + sample_index=index, libraries=libraries, sample=None, library_id=library_id, @@ -1376,8 +1368,13 @@ class RequestsCommon( BaseController, Us # not have ACCESS permissions associated with them (only LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE), so all folders will # be present in the folder_select_field for each library selected. params = util.Params( kwd ) - library_select_field_name= "sample_%i_library_id" % sample_index - folder_select_field_name = "sample_%i_folder_id" % sample_index + if sample_index == 'sample_operation': + # build the library selection widget for the bulk sample operation + library_select_field_name= "sample_operation_library_id" + folder_select_field_name = "sample_operation_folder_id" + else: + library_select_field_name= "sample_%i_library_id" % sample_index + folder_select_field_name = "sample_%i_folder_id" % sample_index if not library_id: library_id = params.get( library_select_field_name, None ) if not folder_id: --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -127,17 +127,14 @@ class DataTransferGrid( grids.Grid ): operations = [ grids.GridOperation( "Transfer", allow_multiple=True, - condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), - url_args=dict( webapp="galaxy" ) ), + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, - condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), - url_args=dict( webapp="galaxy" ) ), + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ), grids.GridOperation( "Delete", allow_multiple=True, - condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ), - url_args=dict( webapp="galaxy" ) ) + condition=( lambda item: item.status in [ model.SampleDataset.transfer_status.NOT_STARTED ] ) ) ] def apply_query_filter( self, trans, query, **kwd ): sample_id = kwd.get( 'sample_id', None ) --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1571,10 +1571,9 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) - lib_widget_index = sample_index + 1 - tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) - self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) - tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) + tc.fv( "1", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) # Do not click on Add sample button when all the sample have been added @@ -1592,10 +1591,9 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) - lib_widget_index = sample_index + 1 - tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) - self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) - tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) + tc.fv( "1", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) tc.submit( "save_samples_button" ) @@ -1631,6 +1629,7 @@ class TwillTestCase( unittest.TestCase ) for sample_id in sample_ids: tc.fv( "1", "select_sample_%i" % sample_id, True ) tc.fv( "1", "sample_operation", 'Change state' ) + # refresh on change to show the sample states selectfield self.refresh_form( "sample_operation", 'Change state' ) self.check_page_for_string( "Change current state" ) tc.fv( "1", "sample_state_id", new_sample_state_id ) @@ -1646,12 +1645,15 @@ class TwillTestCase( unittest.TestCase ) for sample_id in sample_ids: tc.fv( "1", "select_sample_%i" % sample_id, True ) tc.fv( "1", "sample_operation", 'Select data library and folder' ) + # refresh on change to show the data libraries selectfield self.refresh_form( "sample_operation", 'Select data library and folder' ) self.check_page_for_string( "Select data library:" ) - tc.fv( "1", "sample_0_library_id", new_library_id ) - self.refresh_form( "sample_0_library_id", new_library_id ) + tc.fv( "1", "sample_operation_library_id", new_library_id ) + # refresh on change to show the selectfield with the list of + # folders in the selected data library above + self.refresh_form( "sample_operation_library_id", new_library_id ) self.check_page_for_string( "Select folder:" ) - tc.fv( "1", "sample_0_folder_id", new_folder_id ) + tc.fv( "1", "sample_operation_folder_id", new_folder_id ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -72,7 +72,7 @@ <div class="toolFormBody"><div class="form-row"><label>Current state:</label> - ${request.state} + <a href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${request.state}</a><div style="clear: both"></div></div><div class="form-row"> @@ -100,11 +100,7 @@ %><div class="form-row"><label>${field_label}:</label> - %if field_label == 'State': - <a href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> - %else: - ${field_value} - %endif + ${field_value} </div><div style="clear: both"></div> %endfor --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -476,13 +476,7 @@ <th>Name</th> %for index, field in fields_dict.items(): <th> - ${field['label']} - ## TODO: help comments in the grid header are UGLY! - ## If they are needed display them more appropriately, - ## if they are not, delete this commented code. - ##<div class="toolParamHelp" style="clear: both;"> - ## <i>${field['helptext']}</i> - ##</div> + <a class="display tooltip" title="${field['helptext']}" >${field['label']}</a></th> %endfor <th></th>

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galaxy-dist commit 940d77bec4d5: Remove unneeded grid initialization code.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1285797982 14400 # Node ID 940d77bec4d59a5418f9f731ca6ca114d748aa5d # Parent 2aee56b5875a201b09f736764390651a177702d8 Remove unneeded grid initialization code. --- a/templates/tracks/add_tracks.mako +++ b/templates/tracks/add_tracks.mako @@ -5,10 +5,3 @@ ${grid_javascripts()} ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} - -## Initialize the grid. -## TODO: This may not be necessary -- check when adding tracks is working again. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script>

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galaxy-dist commit f60654e287a8: Fix bug that was causing Page item selection grids to be initialized twice and hence causing grid paging to fail.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1285782366 14400 # Node ID f60654e287a8534bbf3aea756064ef2d15600f6d # Parent d681ef7538ed0c2314b3ec6ed9f99050b5a2ef03 Fix bug that was causing Page item selection grids to be initialized twice and hence causing grid paging to fail. --- a/templates/tracks/add_tracks.mako +++ b/templates/tracks/add_tracks.mako @@ -7,6 +7,7 @@ ${render_grid_table( grid, show_item_checkboxes=True )} ## Initialize the grid. +## TODO: This may not be necessary -- check when adding tracks is working again. <script type="text/javascript"> init_grid_elements(); init_grid_controls(); --- a/templates/page/select_items_grid.mako +++ b/templates/page/select_items_grid.mako @@ -5,9 +5,3 @@ ${stylesheets()} ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} - -## Initialize the grid. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script>

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galaxy-dist commit 2aee56b5875a: Updated test outputs for pdf/image output tools that differ slightly on updated dependencies.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1285795531 14400 # Node ID 2aee56b5875a201b09f736764390651a177702d8 # Parent 516a02525898381be3a9af8f3ffec205133dbda1 Updated test outputs for pdf/image output tools that differ slightly on updated dependencies. --- a/test-data/kpca_out2.pdf +++ b/test-data/kpca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310152519) -/ModDate (D:20100310152519) +/CreationDate (D:20100929155208) +/ModDate (D:20100929155208) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 47.81 276.05 240.19 228.24 re W n Q q 0.000 0.000 0.000 RG @@ -1115,7 +1115,7 @@ Q endstream endobj 7 0 obj -22476 +22484 endobj 3 0 obj << @@ -1170,15 +1170,15 @@ 0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000022843 00000 n -0000022926 00000 n +0000022851 00000 n +0000022934 00000 n 0000000213 00000 n 0000000293 00000 n -0000022822 00000 n -0000023030 00000 n -0000023287 00000 n -0000023370 00000 n -0000023467 00000 n +0000022830 00000 n +0000023038 00000 n +0000023295 00000 n +0000023378 00000 n +0000023475 00000 n trailer << /Size 12 @@ -1186,5 +1186,5 @@ trailer /Root 2 0 R >> startxref -23569 +23577 %%EOF --- a/test-data/cca_out2.pdf +++ b/test-data/cca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155029) -/ModDate (D:20100310155029) +/CreationDate (D:20100929152548) +/ModDate (D:20100929152548) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG 0.75 w @@ -400,7 +400,7 @@ Q endstream endobj 7 0 obj -5992 +6000 endobj 8 0 obj << @@ -415,7 +415,7 @@ 9 0 obj /Length 10 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG @@ -788,7 +788,7 @@ Q endstream endobj 10 0 obj -6029 +6037 endobj 3 0 obj << @@ -805,7 +805,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 12 0 R /F3 13 0 R >> -/ExtGState << >> +/ExtGState << /GSais 14 0 R >> >> endobj 11 0 obj @@ -831,28 +831,35 @@ 13 0 obj << /BaseFont /Helvetica-Bold /Encoding 11 0 R >> endobj +14 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 14 +0 15 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000012542 00000 n -0000012631 00000 n +0000012558 00000 n +0000012647 00000 n 0000000213 00000 n 0000000293 00000 n -0000006338 00000 n -0000006358 00000 n -0000006438 00000 n -0000012521 00000 n -0000012724 00000 n -0000012982 00000 n -0000013080 00000 n +0000006346 00000 n +0000006366 00000 n +0000006446 00000 n +0000012537 00000 n +0000012754 00000 n +0000013012 00000 n +0000013110 00000 n +0000013213 00000 n trailer << -/Size 14 +/Size 15 /Info 1 0 R /Root 2 0 R >> startxref -13183 +13263 %%EOF --- a/test-data/q_values.tabular +++ b/test-data/q_values.tabular @@ -1,4 +1,4 @@ -pi0: 0.243863648325618 +pi0: 0.243863648325618 FDR level: 0.05 --- a/test-data/kpca_out4.pdf +++ b/test-data/kpca_out4.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310154313) -/ModDate (D:20100310154313) +/CreationDate (D:20100929160535) +/ModDate (D:20100929160535) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG 0.75 w @@ -549,7 +549,7 @@ Q endstream endobj 7 0 obj -10735 +10743 endobj 3 0 obj << @@ -604,15 +604,15 @@ 0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000011102 00000 n -0000011185 00000 n +0000011110 00000 n +0000011193 00000 n 0000000213 00000 n 0000000293 00000 n -0000011081 00000 n -0000011289 00000 n -0000011546 00000 n -0000011629 00000 n -0000011726 00000 n +0000011089 00000 n +0000011297 00000 n +0000011554 00000 n +0000011637 00000 n +0000011734 00000 n trailer << /Size 12 @@ -620,5 +620,5 @@ trailer /Root 2 0 R >> startxref -11828 +11836 %%EOF --- a/test-data/histogram_out1.pdf +++ b/test-data/histogram_out1.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20091214150037) -/ModDate (D:20091214150037) +/CreationDate (D:20100929153637) +/ModDate (D:20100929153637) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q BT 0.000 0.000 0.000 rg @@ -479,7 +479,7 @@ Q endstream endobj 7 0 obj -7417 +7425 endobj 3 0 obj << @@ -495,7 +495,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R /F3 10 0 R >> -/ExtGState << >> +/ExtGState << /GSais 11 0 R >> >> endobj 8 0 obj @@ -521,25 +521,32 @@ 10 0 obj << /BaseFont /Helvetica-Bold /Encoding 8 0 R >> endobj +11 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 11 +0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000007783 00000 n -0000007866 00000 n +0000007791 00000 n +0000007874 00000 n 0000000213 00000 n 0000000293 00000 n -0000007763 00000 n -0000007958 00000 n -0000008215 00000 n -0000008311 00000 n +0000007771 00000 n +0000007980 00000 n +0000008237 00000 n +0000008333 00000 n +0000008435 00000 n trailer << -/Size 11 +/Size 12 /Info 1 0 R /Root 2 0 R >> startxref -8413 +8485 %%EOF --- a/test-data/pca_out4.pdf +++ b/test-data/pca_out4.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155851) -/ModDate (D:20100310155851) +/CreationDate (D:20100929163248) +/ModDate (D:20100929163248) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 0.000 0.000 0.000 RG 0.75 w @@ -647,7 +647,7 @@ Q endstream endobj 7 0 obj -12853 +12861 endobj 3 0 obj << @@ -663,7 +663,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R >> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,24 +682,31 @@ 9 0 obj << /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000013220 00000 n -0000013303 00000 n +0000013228 00000 n +0000013311 00000 n 0000000213 00000 n 0000000293 00000 n -0000013199 00000 n -0000013384 00000 n -0000013641 00000 n +0000013207 00000 n +0000013406 00000 n +0000013663 00000 n +0000013759 00000 n trailer << -/Size 10 +/Size 11 /Info 1 0 R /Root 2 0 R >> startxref -13737 +13809 %%EOF --- a/test-data/pca_out6.pdf +++ b/test-data/pca_out6.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100914141739) -/ModDate (D:20100914141739) +/CreationDate (D:20100929164125) +/ModDate (D:20100929164125) /Title (R Graphics Output) -/Producer (R 2.11.1) +/Producer (R 2.11.0) /Creator (R) >> endobj Binary file test-data/454Score.png has changed --- a/test-data/regr_out.pdf +++ b/test-data/regr_out.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100603105440) -/ModDate (D:20100603105440) +/CreationDate (D:20100929153009) +/ModDate (D:20100929153009) /Title (R Graphics Output) -/Producer (R 2.9.2) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 38.02 358.66 166.66 160.32 re W n Q q 0.000 0.000 0.000 RG @@ -524,7 +524,7 @@ Q endstream endobj 7 0 obj -9361 +9369 endobj 8 0 obj << @@ -539,7 +539,7 @@ 9 0 obj /Length 10 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -695,7 +695,7 @@ Q endstream endobj 10 0 obj -3090 +3098 endobj 11 0 obj << @@ -710,7 +710,7 @@ 12 0 obj /Length 13 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG @@ -850,7 +850,7 @@ Q endstream endobj 13 0 obj -2841 +2849 endobj 14 0 obj << @@ -865,7 +865,7 @@ 15 0 obj /Length 16 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -1090,7 +1090,7 @@ Q endstream endobj 16 0 obj -4322 +4330 endobj 17 0 obj << @@ -1105,7 +1105,7 @@ 18 0 obj /Length 19 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -1499,7 +1499,7 @@ Q endstream endobj 19 0 obj -6882 +6890 endobj 3 0 obj << @@ -1519,7 +1519,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font << /F1 21 0 R /F2 22 0 R /F3 23 0 R >> -/ExtGState << >> +/ExtGState << /GSais 24 0 R >> >> endobj 20 0 obj @@ -1553,38 +1553,45 @@ 23 0 obj << /BaseFont /Helvetica-Bold /Encoding 20 0 R >> endobj +24 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 24 +0 25 0000000000 65535 f 0000000021 00000 n -0000000163 00000 n -0000027490 00000 n -0000027600 00000 n -0000000212 00000 n -0000000292 00000 n -0000009706 00000 n -0000009726 00000 n -0000009806 00000 n -0000012950 00000 n -0000012971 00000 n -0000013053 00000 n -0000015949 00000 n -0000015970 00000 n -0000016052 00000 n -0000020429 00000 n -0000020450 00000 n -0000020532 00000 n -0000027469 00000 n -0000027705 00000 n -0000027963 00000 n -0000028047 00000 n -0000028145 00000 n +0000000164 00000 n +0000027531 00000 n +0000027641 00000 n +0000000213 00000 n +0000000293 00000 n +0000009715 00000 n +0000009735 00000 n +0000009815 00000 n +0000012967 00000 n +0000012988 00000 n +0000013070 00000 n +0000015974 00000 n +0000015995 00000 n +0000016077 00000 n +0000020462 00000 n +0000020483 00000 n +0000020565 00000 n +0000027510 00000 n +0000027760 00000 n +0000028018 00000 n +0000028102 00000 n +0000028200 00000 n +0000028303 00000 n trailer << -/Size 24 +/Size 25 /Info 1 0 R /Root 2 0 R >> startxref -28248 +28353 %%EOF --- a/test-data/pca_out2.pdf +++ b/test-data/pca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155829) -/ModDate (D:20100310155829) +/CreationDate (D:20100929163120) +/ModDate (D:20100929163120) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 0.000 0.000 0.000 RG 0.75 w @@ -647,7 +647,7 @@ Q endstream endobj 7 0 obj -12848 +12856 endobj 3 0 obj << @@ -663,7 +663,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R >> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,24 +682,31 @@ 9 0 obj << /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000013215 00000 n -0000013298 00000 n +0000013223 00000 n +0000013306 00000 n 0000000213 00000 n 0000000293 00000 n -0000013194 00000 n -0000013379 00000 n -0000013636 00000 n +0000013202 00000 n +0000013401 00000 n +0000013658 00000 n +0000013754 00000 n trailer << -/Size 10 +/Size 11 /Info 1 0 R /Root 2 0 R >> startxref -13732 +13804 %%EOF Binary file test-data/boxplot_summary_statistics_out.png has changed Binary file test-data/solexaScore.png has changed

1 0

galaxy-dist commit a9694088cf69: trackster: Move "Add Tracks" button to main pane, UI tweaks for overview
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1285782969 14400 # Node ID a9694088cf69e31fbd3f940cca497e1d2e366f75 # Parent f60654e287a8534bbf3aea756064ef2d15600f6d trackster: Move "Add Tracks" button to main pane, UI tweaks for overview --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -43,30 +43,12 @@ <div style="float:left;" id="title"></div><a class="panel-header-button right-float" href="${h.url_for( controller='visualization', action='list' )}">Close</a><a id="save-button" class="panel-header-button right-float" href="javascript:void(0);">Save</a> - <a id="refresh-button" class="panel-header-button right-float" href="javascript:void(0);" onclick="view.update_options();return false;">Refresh</a> + <a id="add-track" class="panel-header-button right-float" href="javascript:void(0);">Add Tracks</a></div></div></%def> -<%def name="right_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner">Configuration - <a id="add-track" class="panel-header-button right-float" href="javascript:void(0);">Add Tracks</a> - </div> - </div> - <form action="#" onsubmit="view.update_options();return false;"> - <div id="show-hide-move"> - <div id="no-tracks" class="warningmessage" style="margin: 5px; display:none;"> - There are currently no tracks in this browser. Add tracks via the button above. - </div> - <ul id="sortable-ul"></ul> - </div> - <input type="submit" id="refresh-button" value="Refresh" style="display:none" /> - </form> - -</%def> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -383,7 +383,7 @@ var View = function( container, chrom, t var left_px = ( this.low / (this.max_high - this.max_low) ) * this.overview_viewport.width(); var width_px = (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width(); - this.overview_box.css({ left: left_px, width: Math.max(12, width_px) - 2 }).show(); + this.overview_box.css({ left: left_px, width: Math.max(12, width_px) }).show(); if (this.overview_highlight) { this.overview_highlight.css({ left: left_px, width: width_px }); } --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -6,12 +6,12 @@ .nav-controls a{padding:0 0.4em;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0px 10px;} -.intro{position:absolute;top:50%;left:30%;color:#555;font-size:16px;} +.intro{margin-top:200px;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px;} .overview{width:100%;margin:0px;color:white;} .overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;} .overview-highlight{opacity:0.5;top:0px;position:absolute;z-index:100;border-style:solid;border-color:#6a6;border-width:0px 1px;} -.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#F8F8F8;} -.overview-box{opacity:0.5;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#cfc url(../images/visualization/draggable_horizontal.png) center center no-repeat;border-style:solid;border-color:#6a6;border-width:0px 2px;} +.overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;} +.overview-box{opacity:0.5;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#cfc url(../images/visualization/draggable_horizontal.png) center center no-repeat;border-style:solid;border-color:#6a6;border-width:0px 1px;} .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;} .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;} --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -35,10 +35,11 @@ margin: 0px 10px; } .intro { - position: absolute; - top: 50%; - left: 30%; + margin-top: 200px; + margin-left: auto; + margin-right: auto; color: #555; + text-align: center; font-size: 16px; } .overview { @@ -70,7 +71,7 @@ z-index: 50; position: absolute; height: 14px; - background: #F8F8F8; + background: #eee; } .overview-box { opacity: 0.5; @@ -82,7 +83,7 @@ background: #cfc url(../images/visualization/draggable_horizontal.png) center center no-repeat; border-style: solid; border-color: #6a6; - border-width: 0px 2px; + border-width: 0px 1px; } .viewport-canvas { width: 100%; --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").hide().appendTo(c);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box_background=$("<div/>").addClass("overview-boxback").app endTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hi de();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.content_div.hide();a.chrom_select.bind("change",function (){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.active=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.active){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",f unction(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show();c.content_div.hide()}else{c.intro_div.hide();c.content_div.show()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;i f(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport_container.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".ya xislabel").remove()},redraw:function(h){var d=this.high-this.low,b=this.low,f=this.high;if(b<this.max_low){b=this.max_low}if(f>this.max_high){f=this.max_high}if(this.high!==0&&d<this.min_separation){f=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(f);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var e=(this.low/(this.max_high-this.max_low))*this.overview_viewport.width();var g=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();this.overview_box.css({left:e,width:Math.max(12,g)-2}).show();if(this.overview_highlight){this.overview_highlight.css({left:e,width:g})}this.update_location(this.low,this.high);if(!h){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){thi s.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent _element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}e lse{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set track as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.track s[j].is_overview=false}}};b["Edit configuration"]=function(){show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:function(){hide_modal()},OK:function(){d.update_options(d.track_id);hide_modal()}})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this, k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overview_height);if(this.initial_canvas&&this.is_overview){if(!a.overview_highlight){a.overview_highlight=$("<div />").addClass("overview-highlight").appendTo(a.overview_viewport)}a.overview_viewport.append(this.initial_canvas);a.overview_highlight.height(this.initial_canvas.height());a.overview_vie wport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContex t("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.le ngth;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max _value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution} ,success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRe ct(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.m in_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_colo r!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>" ).get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.r ound(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(aa,l,o,an){var H=l*DENSITY*aa,ag=(l+1)*DENSITY*aa,G=ag-H;var ah=(!this.initial_canvas?"initial":H+"_"+ag);var C=this.data_cache.get(ah);var d;if(C===undefined||(this.mode!=="Auto"&&C.dataset_type==="summary_tree")){this.data_queue[[H,ag]]=true;this.get_data(H,ag);return}var a=Math.ceil(G*an),O=$("<canvas class='tile'></canvas>"),ac=this.prefs.label_color,g=this.prefs.block_color,n=this.mode,r=25,Y=(n==="Squish")||(n==="Dense")&&(n!=="Pack")||(n==="Auto"&&(C.extra_info==="no_detail")),S=this.left_offset,am,v,ao;if(C.dataset_type==="summary_tree"){v=this.summary_draw_height}else{if(n==="Dense"){v=r;ao=10} else{ao=(Y?this.vertical_nodetail_px:this.vertical_detail_px);var s=(an<0.0001?1/view.zoom_res:an);v=this.incremental_slots(s,C.data,Y,n)*ao+r;am=this.inc_slots[s]}}O.css({position:"absolute",top:0,left:(H-this.view.low)*an-S});O.get(0).width=a+S;O.get(0).height=v;o.parent().css("height",Math.max(this.height_px,v)+"px");var D=O.get(0).getContext("2d");D.fillStyle=g;D.font=this.default_font;D.textAlign="right";if(C.dataset_type=="summary_tree"){var N,K=55,af=255-K,h=af*2/3,U=C.data,F=C.max,m=C.avg,b=Math.ceil(C.delta*an);for(var aj=0,B=U.length;aj<B;aj++){var W=Math.floor((U[aj][0]-H)*an);var V=U[aj][1];if(!V){continue}N=Math.floor(af-(V/F)*af);D.fillStyle="rgb("+N+","+N+","+N+")";D.fillRect(W+S,0,b,this.summary_draw_height);if(this.prefs.show_counts&&D.measureText(V).width<b){if(N>h){D.fillStyle="black"}else{D.fillStyle="#ddd"}D.textAlign="center";D.fillText(V,W+S+(b/2),12)}}d="Summary";o.append(O);return O}if(C.message){O.css({border:"solid red","border-width":"2px 2px 2px 0px"});D.fillStyle="red";D.textAlign="left";D.fillText(C.message,100+S,ao)}var al=C.data;var ai=0;for(var aj=0,B=al.length;aj<B;aj++){var P=al[aj],M=P[0],ak=P[1],X=P[2],I=P[3];if(ak<=ag&&X>=H){var Z=Math.floor(Math.max(0,(ak-H)*an)),E=Math.ceil(Math.min(a,Math.max(0,(X-H)*an))),T=(n==="Dense"?1:(1+am[M]))*ao;if(C.dataset_type==="bai"){D.fillStyle=g;if(P[4] instanceof Array){var w=Math.floor(Math.max(0,(P[4][0]-H)*an)),L=Math.ceil(Math.min(a,Math.max(0,(P[4][1]-H)*an))),u=Math.floor(Math.max(0,(P[5][0]-H)*an)),q=Math.ceil(Math.min(a,Math.max(0,(P[5][1]-H)*an)));if(P[4][1]>=H&&P[4][0]<=ag){this.rect_or_text(D,an,H,ag,P[4][0],P[4][2],w+S,L-w,T)}if(P[5][1]>=H&&P[5][0]<=ag){this.rect_or_text(D,an,H,ag,P[5][0],P[5][2],u+S,q-u,T)}if(u>L){D.fillStyle="#999";D.fillRect(L+S,T+5,u-L,1)}}else{D.fillStyle=g;this.rect_or_text(D,an,H,ag,ak,I,Z+S,E-Z,T)}if(n!=="Dense"&&!Y&&ak>H){D.fillStyle=this.prefs.label_color;if(l===0&&Z-D.measureText(I).width<0){D.textAlign="left";D.fillText(M,E+2+S,T+ 8)}else{D.textAlign="right";D.fillText(M,Z-2+S,T+8)}D.fillStyle=g}}else{if(C.dataset_type==="interval_index"){if(Y){D.fillStyle=g;D.fillRect(Z+S,T+5,E-Z,1)}else{var A=P[4],R=P[5],ab=P[6],f=P[7];var z,ad,J=null,ap=null;if(R&&ab){J=Math.floor(Math.max(0,(R-H)*an));ap=Math.ceil(Math.min(a,Math.max(0,(ab-H)*an)))}if(n!=="Dense"&&I!==undefined&&ak>H){D.fillStyle=ac;if(l===0&&Z-D.measureText(I).width<0){D.textAlign="left";D.fillText(I,E+2+S,T+8)}else{D.textAlign="right";D.fillText(I,Z-2+S,T+8)}D.fillStyle=g}if(f){if(A){if(A=="+"){D.fillStyle=RIGHT_STRAND}else{if(A=="-"){D.fillStyle=LEFT_STRAND}}D.fillRect(Z+S,T,E-Z,10);D.fillStyle=g}for(var ah=0,e=f.length;ah<e;ah++){var p=f[ah],c=Math.floor(Math.max(0,(p[0]-H)*an)),Q=Math.ceil(Math.min(a,Math.max((p[1]-H)*an)));if(c>Q){continue}z=5;ad=3;D.fillRect(c+S,T+ad,Q-c,z);if(J!==undefined&&!(c>ap||Q<J)){z=9;ad=1;var ae=Math.max(c,J),t=Math.min(Q,ap);D.fillRect(ae+S,T+ad,t-ae,z)}}}else{z=9;ad=1;D.fillRect(Z+S,T+ad,E-Z,z);if(P.strand){if(P. strand=="+"){D.fillStyle=RIGHT_STRAND_INV}else{if(P.strand=="-"){D.fillStyle=LEFT_STRAND_INV}}D.fillRect(Z+S,T,E-Z,10);D.fillStyle=g}}}}}ai++}}o.append(O);return O},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selecte d").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").hide().appendTo(c);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box_background=$("<div/>").addClass("overview-boxback").app endTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hi de();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.content_div.hide();a.chrom_select.bind("change",function (){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.active=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.active){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",f unction(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show();c.content_div.hide()}else{c.intro_div.hide();c.content_div.show()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;i f(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport_container.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".ya xislabel").remove()},redraw:function(h){var d=this.high-this.low,b=this.low,f=this.high;if(b<this.max_low){b=this.max_low}if(f>this.max_high){f=this.max_high}if(this.high!==0&&d<this.min_separation){f=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(f);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var e=(this.low/(this.max_high-this.max_low))*this.overview_viewport.width();var g=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();this.overview_box.css({left:e,width:Math.max(12,g)}).show();if(this.overview_highlight){this.overview_highlight.css({left:e,width:g})}this.update_location(this.low,this.high);if(!h){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this. label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_e lement.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}els e{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set track as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[ j].is_overview=false}}};b["Edit configuration"]=function(){show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:function(){hide_modal()},OK:function(){d.update_options(d.track_id);hide_modal()}})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k, j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overview_height);if(this.initial_canvas&&this.is_overview){if(!a.overview_highlight){a.overview_highlight=$("<div />").addClass("overview-highlight").appendTo(a.overview_viewport)}a.overview_viewport.append(this.initial_canvas);a.overview_highlight.height(this.initial_canvas.height());a.overview_viewp ort.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext( "2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.leng th;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_v alue))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},s uccess:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect (u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min _value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color! ==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>"). get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.rou nd(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(aa,l,o,an){var H=l*DENSITY*aa,ag=(l+1)*DENSITY*aa,G=ag-H;var ah=(!this.initial_canvas?"initial":H+"_"+ag);var C=this.data_cache.get(ah);var d;if(C===undefined||(this.mode!=="Auto"&&C.dataset_type==="summary_tree")){this.data_queue[[H,ag]]=true;this.get_data(H,ag);return}var a=Math.ceil(G*an),O=$("<canvas class='tile'></canvas>"),ac=this.prefs.label_color,g=this.prefs.block_color,n=this.mode,r=25,Y=(n==="Squish")||(n==="Dense")&&(n!=="Pack")||(n==="Auto"&&(C.extra_info==="no_detail")),S=this.left_offset,am,v,ao;if(C.dataset_type==="summary_tree"){v=this.summary_draw_height}else{if(n==="Dense"){v=r;ao=10}el se{ao=(Y?this.vertical_nodetail_px:this.vertical_detail_px);var s=(an<0.0001?1/view.zoom_res:an);v=this.incremental_slots(s,C.data,Y,n)*ao+r;am=this.inc_slots[s]}}O.css({position:"absolute",top:0,left:(H-this.view.low)*an-S});O.get(0).width=a+S;O.get(0).height=v;o.parent().css("height",Math.max(this.height_px,v)+"px");var D=O.get(0).getContext("2d");D.fillStyle=g;D.font=this.default_font;D.textAlign="right";if(C.dataset_type=="summary_tree"){var N,K=55,af=255-K,h=af*2/3,U=C.data,F=C.max,m=C.avg,b=Math.ceil(C.delta*an);for(var aj=0,B=U.length;aj<B;aj++){var W=Math.floor((U[aj][0]-H)*an);var V=U[aj][1];if(!V){continue}N=Math.floor(af-(V/F)*af);D.fillStyle="rgb("+N+","+N+","+N+")";D.fillRect(W+S,0,b,this.summary_draw_height);if(this.prefs.show_counts&&D.measureText(V).width<b){if(N>h){D.fillStyle="black"}else{D.fillStyle="#ddd"}D.textAlign="center";D.fillText(V,W+S+(b/2),12)}}d="Summary";o.append(O);return O}if(C.message){O.css({border:"solid red","border-width":"2px 2px 2px 0p x"});D.fillStyle="red";D.textAlign="left";D.fillText(C.message,100+S,ao)}var al=C.data;var ai=0;for(var aj=0,B=al.length;aj<B;aj++){var P=al[aj],M=P[0],ak=P[1],X=P[2],I=P[3];if(ak<=ag&&X>=H){var Z=Math.floor(Math.max(0,(ak-H)*an)),E=Math.ceil(Math.min(a,Math.max(0,(X-H)*an))),T=(n==="Dense"?1:(1+am[M]))*ao;if(C.dataset_type==="bai"){D.fillStyle=g;if(P[4] instanceof Array){var w=Math.floor(Math.max(0,(P[4][0]-H)*an)),L=Math.ceil(Math.min(a,Math.max(0,(P[4][1]-H)*an))),u=Math.floor(Math.max(0,(P[5][0]-H)*an)),q=Math.ceil(Math.min(a,Math.max(0,(P[5][1]-H)*an)));if(P[4][1]>=H&&P[4][0]<=ag){this.rect_or_text(D,an,H,ag,P[4][0],P[4][2],w+S,L-w,T)}if(P[5][1]>=H&&P[5][0]<=ag){this.rect_or_text(D,an,H,ag,P[5][0],P[5][2],u+S,q-u,T)}if(u>L){D.fillStyle="#999";D.fillRect(L+S,T+5,u-L,1)}}else{D.fillStyle=g;this.rect_or_text(D,an,H,ag,ak,I,Z+S,E-Z,T)}if(n!=="Dense"&&!Y&&ak>H){D.fillStyle=this.prefs.label_color;if(l===0&&Z-D.measureText(I).width<0){D.textAlign="left";D.fillText(M,E+2+S,T+8) 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1 0

galaxy-dist commit 516a02525898: Move export_history.py script into lib/galaxy/tools/imp_exp so that it's simpler to execute.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1285793202 14400 # Node ID 516a02525898381be3a9af8f3ffec205133dbda1 # Parent a9694088cf69e31fbd3f940cca497e1d2e366f75 Move export_history.py script into lib/galaxy/tools/imp_exp so that it's simpler to execute. --- /dev/null +++ b/lib/galaxy/tools/imp_exp/export_history.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python +""" +Export a history to an archive file using attribute files. + +usage: %prog history_attrs dataset_attrs job_attrs out_file + -G, --gzip: gzip archive file +""" + +from galaxy import eggs +from galaxy.util.json import * +import optparse, sys, os, tempfile, tarfile + +def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ): + """ Create archive from the given attribute/metadata files and save it to out_file. """ + tarfile_mode = "w" + if gzip: + tarfile_mode += ":gz" + try: + + history_archive = tarfile.open( out_file, tarfile_mode ) + + # Read datasets attributes from file. + datasets_attr_in = open( datasets_attrs_file, 'rb' ) + datasets_attr_str = '' + buffsize = 1048576 + try: + while True: + datasets_attr_str += datasets_attr_in.read( buffsize ) + if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: + break + except OverflowError: + pass + datasets_attr_in.close() + datasets_attrs = from_json_string( datasets_attr_str ) + + # Add datasets to archive and update dataset attributes. + # TODO: security check to ensure that files added are in Galaxy dataset directory? + for dataset_attrs in datasets_attrs: + dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name. + dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] ) + history_archive.add( dataset_file_name, arcname=dataset_archive_name ) + # Update dataset filename to be archive name. + dataset_attrs[ 'file_name' ] = dataset_archive_name + + # Rewrite dataset attributes file. + datasets_attrs_out = open( datasets_attrs_file, 'w' ) + datasets_attrs_out.write( to_json_string( datasets_attrs ) ) + datasets_attrs_out.close() + + # Finish archive. + history_archive.add( history_attrs_file, arcname="history_attrs.txt" ) + history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" ) + history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" ) + history_archive.close() + + # Status. + return 'Created history archive.' + except Exception, e: + return 'Error creating history archive: %s' % str( e ), sys.stderr + +if __name__ == "__main__": + # Parse command line. + parser = optparse.OptionParser() + parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' ) + (options, args) = parser.parse_args() + gzip = bool( options.gzip ) + history_attrs, dataset_attrs, job_attrs, out_file = args + + # Create archive. + status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) + print status --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -199,9 +199,10 @@ class JobExportHistoryArchiveWrapper( ob options = "" if jeha.compressed: options = "-G" - return "%s %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), "export_history.sh" ), \ - options, history_attrs_filename, datasets_attrs_filename, \ - jobs_attrs_filename, jeha.dataset.file_name ) + return "python %s %s %s %s %s %s" % ( + os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \ + options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename, \ + jeha.dataset.file_name ) def cleanup_after_job( self, db_session ): """ Remove temporary directory and attribute files generated during setup for this job. """ --- a/scripts/export_history.py +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env python -""" -Export a history to an archive file using attribute files. - -NOTE: This should not be called directly. Use the set_metadata.sh script in Galaxy's -top level directly. - -usage: %prog history_attrs dataset_attrs job_attrs out_file - -G, --gzip: gzip archive file - -D, --delete_dir: delete attribute files' directory if operation completed successfully -""" -from galaxy import eggs -import os, pkg_resources, tempfile, tarfile -pkg_resources.require( "bx-python" ) -import sys, traceback, fileinput -from galaxy.util.json import * -from warnings import warn -from bx.cookbook import doc_optparse - -def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ): - """ Create archive from the given attribute/metadata files and save it to out_file. """ - tarfile_mode = "w" - if gzip: - tarfile_mode += ":gz" - try: - - history_archive = tarfile.open( out_file, tarfile_mode ) - - # Read datasets attributes from file. - datasets_attr_in = open( datasets_attrs_file, 'rb' ) - datasets_attr_str = '' - buffsize = 1048576 - try: - while True: - datasets_attr_str += datasets_attr_in.read( buffsize ) - if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) - - # Add datasets to archive and update dataset attributes. - # TODO: security check to ensure that files added are in Galaxy dataset directory? - for dataset_attrs in datasets_attrs: - dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name. - dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] ) - history_archive.add( dataset_file_name, arcname=dataset_archive_name ) - # Update dataset filename to be archive name. - dataset_attrs[ 'file_name' ] = dataset_archive_name - - # Rewrite dataset attributes file. - datasets_attrs_out = open( datasets_attrs_file, 'w' ) - datasets_attrs_out.write( to_json_string( datasets_attrs ) ) - datasets_attrs_out.close() - - # Finish archive. - history_archive.add( history_attrs_file, arcname="history_attrs.txt" ) - history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" ) - history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" ) - history_archive.close() - - # Status. - return 'Created history archive.' - except Exception, e: - return 'Error creating history archive: %s' + str( e ), sys.stderr - -if __name__ == "__main__": - # Parse command line. - options, args = doc_optparse.parse( __doc__ ) - try: - gzip = bool( options.gzip ) - delete_dir = bool( options.delete_dir ) - history_attrs, dataset_attrs, job_attrs, out_file = args - except: - doc_optparse.exception() - - # Create archive. - status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) - print status --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -54,9 +54,6 @@ class ExportHistoryToolAction( ToolActio job_wrapper = JobExportHistoryArchiveWrapper( job ) cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \ include_deleted=incoming[ 'include_deleted' ] ) - - # Save jeha. - trans.sa_session.flush() # # Add parameters to job_parameter table. --- a/export_history.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python ./scripts/export_history.py $@

1 0

galaxy-dist commit 1ee9e2490e19: Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290013305 18000 # Node ID 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70 # Parent 264c608b48d9b0db2a142d820e32ec1d1fa550dd Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working --- /dev/null +++ b/test-data/tophat_in1.fasta @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --- /dev/null +++ b/test-data/tophat_in2.fastqsanger @@ -0,0 +1,400 @@ +@test_mRNA_150_290_0/1 +TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_197_1/1 +TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/1 +GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_96_238_3/1 +GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/1 +GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/1 +AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/1 +CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/1 +AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_57_231_8/1 +GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/1 +TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_237_a/1 +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/1 +TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/1 +CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/1 +CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_286_e/1 +ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_188_11/1 +TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_218_12/1 +GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/1 +AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_248_14/1 +ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_245_15/1 +AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/1 +AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/1 +ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/1 +AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_212_19/1 +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_11_190_1a/1 +GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_52_261_1b/1 +CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/1 +TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_297_1d/1 +ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/1 +CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_206_1f/1 +TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/1 +GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_235_21/1 +ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/1 +GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_42_209_25/1 +GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_97_275_26/1 +ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/1 +ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_271_28/1 +ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_38_199_29/1 +GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/1 +AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/1 +ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_77_256_2c/1 +GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/1 +CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_65_238_2e/1 +GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_232_2f/1 +GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/1 +AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/1 +AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_131_260_33/1 +GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_240_34/1 +CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_197_35/1 +ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_128_252_36/1 +ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/1 +GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_275_38/1 +TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_207_39/1 +GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/1 +CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_277_3b/1 +ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/1 +CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/1 +GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/1 +CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_193_3f/1 +ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_94_291_40/1 +CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_91_256_41/1 +CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/1 +TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_266_43/1 +GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_250_44/1 +GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/1 +AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_5_197_46/1 +CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_280_48/1 +CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_49/1 +ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_189_4a/1 +AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_78_276_4b/1 +GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/1 +CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_223_4e/1 +ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_172_294_4f/1 +ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/1 +TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_3_187_51/1 +TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/1 +TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_268_53/1 +TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_204_54/1 +ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_41_236_55/1 +AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_56_183_56/1 +GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/1 +AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_271_58/1 +GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_6_182_59/1 +TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/1 +GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/1 +GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_39_219_5c/1 +CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_4_191_5d/1 +CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_259_5e/1 +CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/1 +CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/1 +CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_22_173_62/1 +AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/1 +TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII Binary file test-data/tophat_out1h.bam has changed --- a/test-data/tophat_in1.fq +++ /dev/null @@ -1,400 +0,0 @@ -@test_mRNA_150_290_0/1 -TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_197_1/1 -TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_255_2/1 -GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_96_238_3/1 -GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_72_258_4/1 -GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_107_286_5/1 -AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_122_299_6/1 -CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_234_7/1 -AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_57_231_8/1 -GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_155_9/1 -TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_237_a/1 -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_230_b/1 -TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_276_c/1 -CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_268_d/1 -CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_286_e/1 -ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_118_297_f/1 -AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_16_194_10/1 -TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_188_11/1 -TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_218_12/1 -GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_266_13/1 -AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_248_14/1 -ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_245_15/1 -AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_218_16/1 -AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_195_17/1 -ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_126_282_18/1 -AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_212_19/1 -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_11_190_1a/1 -GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_52_261_1b/1 -CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_274_1c/1 -TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_297_1d/1 -ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_225_1e/1 -CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_206_1f/1 -TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_249_20/1 -GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_235_21/1 -ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_267_22/1 -CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_69_229_23/1 -ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_21_208_24/1 -GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_42_209_25/1 -GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_97_275_26/1 -ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_146_27/1 -ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_271_28/1 -ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_38_199_29/1 -GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_103_284_2a/1 -AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_271_2b/1 -ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_77_256_2c/1 -GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_50_224_2d/1 -CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_65_238_2e/1 -GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_232_2f/1 -GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_26_189_30/1 -AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_79_256_31/1 -AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_267_32/1 -CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_131_260_33/1 -GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_240_34/1 -CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_197_35/1 -ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_128_252_36/1 -ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_145_300_37/1 -GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_275_38/1 -TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_207_39/1 -GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_228_3a/1 -CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_277_3b/1 -ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_30_231_3c/1 -CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_220_3d/1 -GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_278_3e/1 -CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_193_3f/1 -ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_94_291_40/1 -CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_91_256_41/1 -CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_23_186_42/1 -TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_266_43/1 -GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_250_44/1 -GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_106_253_45/1 -AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_5_197_46/1 -CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_47/1 -TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_280_48/1 -CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_49/1 -ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_189_4a/1 -AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_78_276_4b/1 -GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_63_229_4c/1 -ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_245_4d/1 -CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_223_4e/1 -ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_172_294_4f/1 -ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_88_257_50/1 -TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_3_187_51/1 -TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_9_179_52/1 -TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_268_53/1 -TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_204_54/1 -ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_41_236_55/1 -AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_56_183_56/1 -GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_250_57/1 -AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_271_58/1 -GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_6_182_59/1 -TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_272_5a/1 -GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_114_277_5b/1 -GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_39_219_5c/1 -CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_4_191_5d/1 -CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_259_5e/1 -CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_279_5f/1 -CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_293_60/1 -CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_297_61/1 -AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_22_173_62/1 -AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_295_63/1 -TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -30,7 +30,7 @@ def __main__(): parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) - + # Options for supplying own junctions parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \ TopHat will use the exon records in this file to build \ @@ -58,18 +58,18 @@ def __main__(): parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' ) parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) - + # Wrapper options. parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) parser.add_option( '', '--single-paired', dest='single_paired', help='' ) parser.add_option( '', '--settings', dest='settings', help='' ) - + (options, args) = parser.parse_args() - + # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() - if options.own_file != 'None': + if options.own_file: index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] ) cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path ) try: @@ -98,12 +98,12 @@ def __main__(): stop_err( 'Error indexing reference sequence\n' + str( e ) ) else: index_path = options.index_path - + # Build tophat command. tmp_output_dir = tempfile.mkdtemp() cmd = 'tophat -o %s %s %s %s' reads = options.input1 - if options.input2 != 'None': + if options.input2: reads += ' ' + options.input2 opts = '-p %s' % options.num_threads if options.single_paired == 'paired': @@ -129,7 +129,7 @@ def __main__(): opts += ' -j %s' % options.raw_juncs if options.no_novel_juncs: opts += ' --no-novel-juncs' - + # Search type options. if options.coverage_search: opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron ) @@ -143,13 +143,13 @@ def __main__(): opts += ' --microexon-search' if options.single_paired == 'paired': opts += ' --mate-std-dev %s' % options.mate_std_dev - if options.seg_mismatches != None: + if options.seg_mismatches: opts += ' --segment-mismatches %d' % int(options.seg_mismatches) - if options.seg_length != None: + if options.seg_length: opts += ' --segment-length %d' % int(options.seg_length) - if options.min_segment_intron != None: + if options.min_segment_intron: opts += ' --min-segment-intron %d' % int(options.min_segment_intron) - if options.max_segment_intron != None: + if options.max_segment_intron: opts += ' --max-segment-intron %d' % int(options.max_segment_intron) cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) except Exception, e: @@ -160,7 +160,7 @@ def __main__(): shutil.rmtree( tmp_output_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) print cmd - + # Run try: tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name @@ -185,10 +185,10 @@ def __main__(): tmp_stderr.close() if returncode != 0: raise Exception, stderr - + # TODO: look for errors in program output. - - # Copy output files from tmp directory to specified files. + + # Copy output files from tmp directory to specified files. shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file ) except Exception, e: --- a/test-data/tophat_in2.fq +++ /dev/null @@ -1,400 +0,0 @@ -@test_mRNA_150_290_0/2 -TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_197_1/2 -GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_255_2/2 -GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_96_238_3/2 -GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_72_258_4/2 -ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_107_286_5/2 -TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_122_299_6/2 -GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_234_7/2 -GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_57_231_8/2 -CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_155_9/2 -TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_237_a/2 -ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_230_b/2 -AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_276_c/2 -ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_268_d/2 -CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_286_e/2 -AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_118_297_f/2 -GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_16_194_10/2 -GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_188_11/2 -GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_218_12/2 -AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_266_13/2 -ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_248_14/2 -TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_245_15/2 -CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_218_16/2 -GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_195_17/2 -GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_126_282_18/2 -GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_212_19/2 -TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_11_190_1a/2 -AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_52_261_1b/2 -CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_274_1c/2 -GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_297_1d/2 -AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_225_1e/2 -ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_206_1f/2 -AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_249_20/2 -GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_235_21/2 -CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_267_22/2 -ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_69_229_23/2 -AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_21_208_24/2 -GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_42_209_25/2 -AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_97_275_26/2 -CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_146_27/2 -GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_271_28/2 -ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_38_199_29/2 -GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_103_284_2a/2 -CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_271_2b/2 -TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_77_256_2c/2 -AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_50_224_2d/2 -CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_65_238_2e/2 -GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_232_2f/2 -TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_26_189_30/2 -GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_79_256_31/2 -ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_267_32/2 -AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_131_260_33/2 -AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_240_34/2 -CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_197_35/2 -GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_128_252_36/2 -AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_145_300_37/2 -GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_275_38/2 -CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_207_39/2 -TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_228_3a/2 -GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_277_3b/2 -GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_30_231_3c/2 -GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_220_3d/2 -GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_278_3e/2 -GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_193_3f/2 -CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_94_291_40/2 -GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_91_256_41/2 -AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_23_186_42/2 -GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_266_43/2 -GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_250_44/2 -AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_106_253_45/2 -CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_5_197_46/2 -GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_47/2 -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_280_48/2 -TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_49/2 -CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_189_4a/2 -ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_78_276_4b/2 -CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_63_229_4c/2 -ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_245_4d/2 -GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_223_4e/2 -GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_172_294_4f/2 -CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_88_257_50/2 -GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_3_187_51/2 -CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_9_179_52/2 -CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_268_53/2 -CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_204_54/2 -TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_41_236_55/2 -TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_56_183_56/2 -ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_250_57/2 -AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_271_58/2 -ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_6_182_59/2 -CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_272_5a/2 -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_114_277_5b/2 -TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_39_219_5c/2 -AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_4_191_5d/2 -ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_259_5e/2 -AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_279_5f/2 -AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_293_60/2 -CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_297_61/2 -CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_22_173_62/2 -GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_295_63/2 -TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- /dev/null +++ b/test-data/tophat_out1j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- a/test-data/tophat_out1.bed +++ /dev/null @@ -1,3 +0,0 @@ -track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_out2j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_out3j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_in3.fastqsanger @@ -0,0 +1,400 @@ +@test_mRNA_150_290_0/2 +TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_197_1/2 +GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/2 +GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_96_238_3/2 +GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/2 +ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/2 +TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/2 +GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/2 +GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_57_231_8/2 +CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/2 +TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_237_a/2 +ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/2 +AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/2 +CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_286_e/2 +AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/2 +GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/2 +GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_188_11/2 +GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_218_12/2 +AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_248_14/2 +TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_245_15/2 +CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/2 +GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/2 +GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/2 +GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_212_19/2 +TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_11_190_1a/2 +AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_52_261_1b/2 +CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/2 +GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_297_1d/2 +AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/2 +ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_206_1f/2 +AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/2 +GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_235_21/2 +CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/2 +ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/2 +AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/2 +GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_42_209_25/2 +AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_97_275_26/2 +CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/2 +GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_271_28/2 +ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_38_199_29/2 +GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/2 +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_77_256_2c/2 +AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/2 +CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_65_238_2e/2 +GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_232_2f/2 +TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/2 +GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/2 +ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/2 +AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_131_260_33/2 +AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_240_34/2 +CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_197_35/2 +GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_128_252_36/2 +AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/2 +GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_275_38/2 +CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_207_39/2 +TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/2 +GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_277_3b/2 +GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/2 +GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/2 +GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/2 +GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_193_3f/2 +CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_94_291_40/2 +GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_91_256_41/2 +AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/2 +GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_266_43/2 +GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_250_44/2 +AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/2 +CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_5_197_46/2 +GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/2 +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_280_48/2 +TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_49/2 +CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_189_4a/2 +ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_78_276_4b/2 +CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/2 +ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/2 +GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_223_4e/2 +GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_172_294_4f/2 +CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/2 +GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_3_187_51/2 +CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/2 +CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_268_53/2 +CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_204_54/2 +TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_41_236_55/2 +TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_56_183_56/2 +ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/2 +AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_271_58/2 +ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_6_182_59/2 +CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/2 +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/2 +TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_39_219_5c/2 +AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_4_191_5d/2 +ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_259_5e/2 +AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/2 +AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/2 +CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/2 +CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_22_173_62/2 +GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="tophat" name="Tophat" version="1.1.2"> +<tool id="tophat" name="Tophat" version="1.2.0"><description>Find splice junctions using RNA-seq data</description><requirements><requirement type="package">tophat</requirement> @@ -7,46 +7,41 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. --num-threads="4" - + ## Provide outputs. --junctions-output=$junctions --hits-output=$accepted_hits - + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile - --indexes-path="None" #else: - --own-file="None" - --indexes-path=$refGenomeSource.index + --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" #end if - + ## Are reads single-end or paired? --single-paired=$singlePaired.sPaired - + ## First input file always required. --input1=$singlePaired.input1 - + ## Set parms based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": - --input2="None" - -r "None" - --settings=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --mate-std-dev="None" - -a $singlePaired.sParams.anchor_length - -m $singlePaired.sParams.splice_mismatches - -i $singlePaired.sParams.min_intron_length - -I $singlePaired.sParams.max_intron_length - -F $singlePaired.sParams.junction_filter - -g $singlePaired.sParams.max_multihits - --min-segment-intron $singlePaired.sParams.min_segment_intron - --max-segment-intron $singlePaired.sParams.max_segment_intron - --seg-mismatches=$singlePaired.sParams.seg_mismatches - --seg-length=$singlePaired.sParams.seg_length - - ## Supplying junctions parameters. - #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": + --settings=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + -a $singlePaired.sParams.anchor_length + -m $singlePaired.sParams.splice_mismatches + -i $singlePaired.sParams.min_intron_length + -I $singlePaired.sParams.max_intron_length + -F $singlePaired.sParams.junction_filter + -g $singlePaired.sParams.max_multihits + --min-segment-intron $singlePaired.sParams.min_segment_intron + --max-segment-intron $singlePaired.sParams.max_segment_intron + --seg-mismatches=$singlePaired.sParams.seg_mismatches + --seg-length=$singlePaired.sParams.seg_length + + ## Supplying junctions parameters. + #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes": -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model #end if @@ -57,47 +52,47 @@ #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes": --no-novel-juncs #end if - #end if - - #if $singlePaired.sParams.closure_search.use_search == "Yes": + #end if + + #if $singlePaired.sParams.closure_search.use_search == "Yes": --closure-search --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron - #else: + #else: --no-closure-search - #end if - #if $singlePaired.sParams.coverage_search.use_search == "Yes": + #end if + #if $singlePaired.sParams.coverage_search.use_search == "Yes": --coverage-search --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron - #else: + #else: --no-coverage-search - #end if - ## TODO: No idea why the type conversion is necessary, but it seems to be. - #if str($singlePaired.sParams.microexon_search) == "Yes": + #end if + ## TODO: No idea why the type conversion is necessary, but it seems to be. + #if str($singlePaired.sParams.microexon_search) == "Yes": --microexon-search - #end if - #end if - #else: - --input2=$singlePaired.input2 - -r $singlePaired.mate_inner_distance - --settings=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --mate-std-dev=$singlePaired.pParams.mate_std_dev - -a $singlePaired.pParams.anchor_length - -m $singlePaired.pParams.splice_mismatches - -i $singlePaired.pParams.min_intron_length - -I $singlePaired.pParams.max_intron_length - -F $singlePaired.pParams.junction_filter - -g $singlePaired.pParams.max_multihits - --min-segment-intron $singlePaired.pParams.min_segment_intron - --max-segment-intron $singlePaired.pParams.max_segment_intron - --seg-mismatches=$singlePaired.pParams.seg_mismatches - --seg-length=$singlePaired.pParams.seg_length - - ## Supplying junctions parameters. - #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": + #end if + #end if + #else: + --input2=$singlePaired.input2 + -r $singlePaired.mate_inner_distance + --settings=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --mate-std-dev=$singlePaired.pParams.mate_std_dev + -a $singlePaired.pParams.anchor_length + -m $singlePaired.pParams.splice_mismatches + -i $singlePaired.pParams.min_intron_length + -I $singlePaired.pParams.max_intron_length + -F $singlePaired.pParams.junction_filter + -g $singlePaired.pParams.max_multihits + --min-segment-intron $singlePaired.pParams.min_segment_intron + --max-segment-intron $singlePaired.pParams.max_segment_intron + --seg-mismatches=$singlePaired.pParams.seg_mismatches + --seg-length=$singlePaired.pParams.seg_length + + ## Supplying junctions parameters. + #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes": -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model #end if @@ -108,29 +103,29 @@ #if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes": --no-novel-juncs #end if - #end if - - #if $singlePaired.pParams.closure_search.use_search == "Yes": + #end if + + #if $singlePaired.pParams.closure_search.use_search == "Yes": --closure-search --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron - #else: + #else: --no-closure-search - #end if - #if $singlePaired.pParams.coverage_search.use_search == "Yes": + #end if + #if $singlePaired.pParams.coverage_search.use_search == "Yes": --coverage-search --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron - #else: + #else: --no-coverage-search - #end if - ## TODO: No idea why the type conversion is necessary, but it seems to be. - #if str ($singlePaired.pParams.microexon_search) == "Yes": + #end if + ## TODO: No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.pParams.microexon_search) == "Yes": --microexon-search #end if - #end if - #end if + #end if + #end if </command><inputs><conditional name="refGenomeSource"> @@ -140,10 +135,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="tophat_indexes" /></param></when><when value="history"> @@ -186,7 +178,7 @@ <conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -196,7 +188,7 @@ <conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -242,7 +234,7 @@ </param></when></conditional> - </when> + </when><when value="paired"><param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> @@ -276,7 +268,7 @@ <conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -286,7 +278,7 @@ <conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -325,14 +317,14 @@ <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /></when><when value="No" /> - </conditional> + </conditional><param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option></param></when></conditional> - </when> + </when></conditional></inputs> @@ -342,38 +334,46 @@ </outputs><tests> - + <test> +  -<test> +  + <param name="genomeSource" value="history" /> + <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /> + <param name="sPaired" value="paired" /> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /> + <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /> + <param name="mate_inner_distance" value="20" /> + <param name="pSettingsType" value="preSet" /> + <output name="junctions" file="tophat_out2j.bed" ftype="bed" /> + <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" ftype="bam" /> + </test> +  + <test> + <param name="genomeSource" value="history"/> - <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/> - <param name="sPaired" value="paired"/> - <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/> - <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/> - <param name="mate_inner_distance" value="20"/> - <param name="pSettingsType" value="preSet"/> - <output name="junctions" file="tophat_out1.bed"/> -  - <output name="accepted_hits" file="tophat_out2.bam" lines_diff="100000"/> - </test> - + <test> +  - -</tests> + </tests><help> **Tophat Overview** Binary file test-data/tophat_out3h.bam has changed Binary file test-data/tophat_out2.bam has changed --- a/test-data/tophat_in3.fa +++ /dev/null @@ -1,14 +0,0 @@ ->test_chromosome -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC -AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT -ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -1,3 +1,4 @@ +<tables><table name="all_fasta" comment_char="#"> @@ -34,7 +35,7 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/bwa_index.loc" /></table> -  + <table name="indexed_maf_files"><columns>name, value, dbkey, species</columns><file path="tool-data/maf_index.loc" /> @@ -65,9 +66,8 @@ <file path="tool-data/srma_index.loc" /></table> -</tables> Binary file test-data/tophat_out4h.bam has changed --- /dev/null +++ b/test-data/tophat_out4j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 Binary file test-data/tophat_out2h.bam has changed

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galaxy-dist commit 5ec30f459e8e: Merge with d1baa724b393de6871df7249ebe35ecfe2054e31
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011973 18000 # Node ID 5ec30f459e8e4a1186f666f4879e14f082f17352 # Parent 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent d1baa724b393de6871df7249ebe35ecfe2054e31 Merge with d1baa724b393de6871df7249ebe35ecfe2054e31

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galaxy-dist commit 7d46c23bb276: Merge with 39f41821aa4eec15b04509d24715946552bb14a6
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011867 18000 # Node ID 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent 8ce82d60b2ab55966d133db136fcb2f809201c4b # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Merge with 39f41821aa4eec15b04509d24715946552bb14a6

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galaxy-dist commit 264c608b48d9: Fixed inconsistency in PerM loc.sample files
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290012220 18000 # Node ID 264c608b48d9b0db2a142d820e32ec1d1fa550dd # Parent 5ec30f459e8e4a1186f666f4879e14f082f17352 Fixed inconsistency in PerM loc.sample files --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -21,8 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -# +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index

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galaxy-dist commit d1baa724b393: Modified some test fastq files to make valid
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290011865 18000 # Node ID d1baa724b393de6871df7249ebe35ecfe2054e31 # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Modified some test fastq files to make valid --- a/test-data/bwa_wrapper_in2.fastq +++ b/test-data/bwa_wrapper_in2.fastq @@ -1,120 +1,120 @@ @seq1/1 GGACTCAGATAGTAATCC -+/1 ++ II#IIIIIII$5+.(9II @seq2/1 ATTCGACCTATCCTTGCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq3/1 GTAACAAAGTTTGGATTG -+/1 ++ IIIIIIIIIIIIIIIIII @seq4/1 AGCCGCTCGTCTTTTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq5/1 CAGTTATATGGCTTTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq6/1 AGGCGCTCGTCTTGGTAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq7/1 TGTAGGTGGTCAACCAAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq8/1 ACACCCGTCCTTTACGTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq9/1 GCCGCTATTCAGGTTGTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq10/1 ATTCTTTCTTTTCGTATC -+/1 ++ IIIIIIIIIIIIIIIIII @seq11/1 GCATTTCTACTCCTTCTC -+/1 ++ II#IIIIIII$5+.(9II @seq12/1 CGCGCTTCGATAAAAATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq13/1 ATTTCTACTCTTTCTCAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq14/1 CCCTTTTGAATGTCACGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq15/1 CCAACTTACCAAGGTGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq16/1 TCAGGGTATTAAAAGAGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq17/1 GTGATGTGCTTGCTACCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq18/1 TCAATCCCCCATGCTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq19/1 TTCCTGCGCTTAATGCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq20/1 CTTATTACCATTTCAACT -+/1 ++ IIIIIIIIIIIIIIIIII @seq21/1 CTGATACCAATAAAACCC -+/1 ++ II#IIIIIII$5+.(9II @seq22/1 AATCAAACTTACCAAGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq23/1 TGTGCTTCCCCAACTTGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq24/1 TTTCTCAATCCCCAATGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq25/1 TTGCTACTGACCGCTCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq26/1 CCGCGTGAAATTTCTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq27/1 CGCTAATCAAGTTGTTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq28/1 AAAGAGATTATTTGTCGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq29/1 CAAATTAATGCGCGCTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq30/1 ATCCCCTATGCTTGGCTT -+/1 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bwa_wrapper_in3.fastq +++ b/test-data/bwa_wrapper_in3.fastq @@ -1,74 +1,74 @@ @seq1/2 ACGCTCCTTTAAAATATC -+/2 ++ IIIII$%*$G$A31I&&B @seq2/2 CAGCTCGAGAAGCTCTTA -+/2 ++ IIIIIIIIIIIIIIIIII @seq3/2 CTACTGACCGCTCTCGTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq4/2 TAGGTGGTCAACCATTTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq5/2 TTTCTATGTGGCTTAATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq6/2 GTAGGTGGTCAACAATTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq7/2 TTTAATTGCAGGGGCTTC -+/2 ++ IIIIIIIIIIIIIIIIII @seq8/2 ATGCGCTCTATTCTCTGG -+/2 ++ IIIIIIIIIIIIIIIIII @seq9/2 TTCTGTTGGTGCTGATAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq10/2 AGGGCGTTGAGTTCGATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq11/2 ATCCCCAATGCTTGGCTT -+/2 ++ IIIII$%*$G$A31I&&B @seq12/2 GGATTGGCGTTTCCAACC -+/2 ++ IIIIIIIIIIIIIIIIII @seq13/2 CCCCAATCCTTGCCTTCC -+/2 ++ IIIAAIIIIIIIIIIIII @seq14/2 TGATATTTTGACTTTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq15/2 TTACGAAACGCGACGCCG -+/2 ++ IIIIIIIIIIIIIIIIII @seq16/2 TTATTTTTCTCCAGCCAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq17/2 AAACAATACTTTAGGCAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq18/2 CCGTTCCATAAGCAGATG -+/2 ++ IIIIIIIIIIIIIIIIII @seq19/2 GAGCGTCCTGGTGCTGAT @@ -76,45 +76,45 @@ GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII @seq20/2 ACTCCGGTTATCGCTGGC -+/2 ++ IIIIIIIIIIIIIIIIII @seq21/2 TAAGCATTTGGTTCAGGG -+/2 ++ IIIII$%*$G$A31I&&B @seq22/2 GTTACGACGCGACGCCGT -+/2 ++ IIIIIIIIIIIIIIIIII @seq23/2 TTTAATAACCCTATAGAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq24/2 CTTGGCTTCCCTAAGCAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq25/2 CGTGCTCGTTGCTGCGTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq26/2 AAGGATGTTTTCCGTTCT -+/2 ++ IIIIIIIIIIIIIIIIII @seq27/2 TGTTTGGTGCTGATATTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq28/2 TCCAGCCACTAAAGTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq29/2 GATAATGATTGGGGTATC -+/2 ++ IIIIIIIIIIIIIIIIII @seq30/2 ACCATAAGCAGATGGATA -+/2 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bowtie_in2.fastqsanger +++ b/test-data/bowtie_in2.fastqsanger @@ -1,5 +1,5 @@ @HWI-EAS91_1_30788AAXX:1:1:1513:715/1 GTTTTTTNNGCATAGATGTTTAGTTGTGGTAGTCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I

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galaxy-dist commit 19b10fff1335: More bug fixes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290010215 18000 # Node ID 19b10fff133595cb5cd1851a7f24024c2637ad2b # Parent 918a25ed14f5427f70970b0c436159fc58fd111e More bug fixes. --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -602,7 +602,7 @@ class Forms( BaseController ): self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: for ft in trans.model.FormDefinition.supported_field_types: - self.fieldtype.add_option( ft.__name__, ft__name__ ) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) @@ -713,7 +713,7 @@ class Forms( BaseController ): form_details=form_details, field_details=field_details, form_definition=form_definition, - field_types=BaseField.form_field_types(), + field_types=trans.model.FormDefinition.supported_field_types, message=message, status=status, current_form_type=current_form[ 'type' ],

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