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[hg] galaxy 3355: On edit attributes page, only sanitize and add...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/26f01eafc6bd changeset: 3355:26f01eafc6bd user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Feb 08 11:20:44 2010 -0500 description: On edit attributes page, only sanitize and add annotation when it exists. Metadata editing was throwing server error when not logged in. diffstat: lib/galaxy/web/controllers/root.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (15 lines): diff -r 4e8785b6815c -r 26f01eafc6bd lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Feb 08 10:00:30 2010 -0500 +++ b/lib/galaxy/web/controllers/root.py Mon Feb 08 11:20:44 2010 -0500 @@ -307,8 +307,9 @@ setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_setting_metadata( data ) # Sanitize annotation before adding it. - annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans, data, annotation ) + if params.annotation: + annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, data, annotation ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' trans.sa_session.flush()

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[hg] galaxy 3354: Fix from Assaf Gordon for Cheetah syntax error...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e8785b6815c changeset: 3354:4e8785b6815c user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Feb 08 10:00:30 2010 -0500 description: Fix from Assaf Gordon for Cheetah syntax errors in the Bar Chart tool. diffstat: tools/plotting/bar_chart.py | 1 - tools/plotting/bar_chart.xml | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diffs (25 lines): diff -r 390dfb039df7 -r 4e8785b6815c tools/plotting/bar_chart.py --- a/tools/plotting/bar_chart.py Mon Feb 08 09:53:20 2010 -0500 +++ b/tools/plotting/bar_chart.py Mon Feb 08 10:00:30 2010 -0500 @@ -23,7 +23,6 @@ """ -from Numeric import * import Gnuplot, Gnuplot.funcutils import sys, string, tempfile, os diff -r 390dfb039df7 -r 4e8785b6815c tools/plotting/bar_chart.xml --- a/tools/plotting/bar_chart.xml Mon Feb 08 09:53:20 2010 -0500 +++ b/tools/plotting/bar_chart.xml Mon Feb 08 10:00:30 2010 -0500 @@ -1,8 +1,8 @@ <tool id="barchart_gnuplot" name="Bar chart"> <description>for multiple columns</description> <command interpreter="python"> - #if $xtic.userSpecified == "Yes": #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" - #else: #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" + #if $xtic.userSpecified == "Yes" #bar_chart.py $input $xtic.xticColumn $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" + #else #bar_chart.py $input 0 $colList "$title" "$ylabel" $ymin $ymax $out_file1 "$pdf_size" #end if </command> <inputs>

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[hg] galaxy 3353: Refactoring grid code: moved numerous grid col...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/390dfb039df7 changeset: 3353:390dfb039df7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 08 09:53:20 2010 -0500 description: Refactoring grid code: moved numerous grid column definitions from controller.py to grids.py diffstat: lib/galaxy/web/base/controller.py | 83 -------------------------- lib/galaxy/web/controllers/admin.py | 6 +- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 8 +- lib/galaxy/web/controllers/library_admin.py | 2 +- lib/galaxy/web/controllers/page.py | 28 ++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 4 +- lib/galaxy/web/controllers/workflow.py | 4 +- lib/galaxy/web/framework/helpers/grids.py | 89 ++++++++++++++++++++++++++- 10 files changed, 113 insertions(+), 115 deletions(-) diffs (465 lines): diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Feb 08 09:53:20 2010 -0500 @@ -9,41 +9,10 @@ from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.web.framework.helpers import grids -from galaxy.util.odict import odict from Cheetah.Template import Template log = logging.getLogger( __name__ ) - -# Useful columns in many grids used by controllers. - -class OwnerColumn( grids.TextColumn ): - """ Column that lists item's owner. """ - def get_value( self, trans, grid, item ): - return item.user.username - -class PublicURLColumn( grids.TextColumn ): - """ Column displays item's public URL based on username and slug. """ - def get_link( self, trans, grid, item ): - if item.user.username and item.slug: - return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - elif not item.user.username: - # TODO: provide link to set username. - return None - elif not item.user.slug: - # TODO: provide link to set slg - return None - -class DeletedColumn( grids.GridColumn ): - """ Column that tracks and filters for items with deleted attribute. """ - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class BaseController( object ): """ @@ -138,58 +107,6 @@ return True Root = BaseController - -class SharingStatusColumn( grids.GridColumn ): - """ Grid column to indicate sharing status. """ - def get_value( self, trans, grid, item ): - # Delete items cannot be shared. - if item.deleted: - return "" - - # Build a list of sharing for this item. - sharing_statuses = [] - if item.users_shared_with: - sharing_statuses.append( "Shared" ) - if item.importable: - sharing_statuses.append( "Accessible" ) - if item.published: - sharing_statuses.append( "Published" ) - return ", ".join( sharing_statuses ) - - def get_link( self, trans, grid, item ): - if not item.deleted and ( item.users_shared_with or item.importable or item.published ): - return dict( operation="share or publish", id=item.id ) - return None - - def filter( self, db_session, user, query, column_filter ): - """ Modify query to filter histories by sharing status. """ - if column_filter == "All": - pass - elif column_filter: - if column_filter == "private": - query = query.filter( self.model_class.users_shared_with == None ) - query = query.filter( self.model_class.importable == False ) - elif column_filter == "shared": - query = query.filter( self.model_class.users_shared_with != None ) - elif column_filter == "accessible": - query = query.filter( self.model_class.importable == True ) - elif column_filter == "published": - query = query.filter( self.model_class.published == True ) - return query - - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = odict() - accepted_filter_labels_and_vals["private"] = "private" - accepted_filter_labels_and_vals["shared"] = "shared" - accepted_filter_labels_and_vals["accessible"] = "accessible" - accepted_filter_labels_and_vals["published"] = "published" - accepted_filter_labels_and_vals["all"] = "All" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class Sharable: """ Mixin for a controller that manages and item that can be shared. """ diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -71,7 +71,7 @@ LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -159,7 +159,7 @@ UsersColumn( "Users", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -225,7 +225,7 @@ RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,7 +44,7 @@ model_class=model.FormDefinition, filterable="advanced" ), TypeColumn( "Type" ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,11 +44,11 @@ attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( @@ -118,7 +118,7 @@ return query.filter( model.HistoryUserShareAssociation.user == trans.user ) class HistoryAllPublishedGrid( grids.Grid ): - class NameURLColumn( PublicURLColumn, NameColumn ): + class NameURLColumn( grids.PublicURLColumn, NameColumn ): pass title = "Published Histories" @@ -128,7 +128,7 @@ use_async = True columns = [ NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -52,7 +52,7 @@ grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:53:20 2010 -0500 @@ -16,7 +16,7 @@ class PageListGrid( grids.Grid ): # Custom column. - class URLColumn( PublicURLColumn ): + class URLColumn( grids.PublicURLColumn ): def get_value( self, trans, grid, item ): return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) @@ -30,7 +30,7 @@ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -62,8 +62,8 @@ default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] @@ -100,8 +100,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -144,8 +144,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -167,8 +167,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -192,8 +192,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -212,8 +212,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:53:20 2010 -0500 @@ -95,7 +95,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), TypeColumn( "Type" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -107,7 +107,7 @@ TypeColumn( "Type", link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ), ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -184,7 +184,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.request_form.id ) ) ), ), SampleFormColumn( "Sample Form", link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.sample_form.id ) ) ), ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:53:20 2010 -0500 @@ -59,8 +59,8 @@ default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:53:20 2010 -0500 @@ -5,6 +5,7 @@ from galaxy.tags.tag_handler import TagHandler from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.odict import odict import sys, logging, math @@ -329,8 +330,8 @@ accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters -# Generic column that employs freetext and, hence, supports freetext, case-independent filtering. class TextColumn( GridColumn ): + """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ def filter( self, db_session, user, query, column_filter ): """ Modify query to filter using free text, case independence. """ if column_filter == "All": @@ -350,8 +351,8 @@ clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) return and_( *clause_list ) -# Column that supports community tags. class CommunityTagsColumn( TextColumn ): + """ Column that supports community tags. """ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class @@ -386,8 +387,8 @@ clause_list.append( self.model_class.tags.any( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ) ) ) return and_( *clause_list ) -# Column that supports individual tags. class IndividualTagsColumn( CommunityTagsColumn ): + """ Column that supports individual tags. """ def get_value( self, trans, grid, item ): return trans.fill_template( "/tagging_common.mako", tag_type="individual", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter" ) @@ -408,8 +409,8 @@ clause_list.append( self.model_class.tags.any( and_( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ), self.model_tag_association_class.user == user ) ) ) return and_( *clause_list ) -# Column that performs multicolumn filtering. class MulticolFilterColumn( TextColumn ): + """ Column that performs multicolumn filtering. """ def __init__( self, col_name, cols_to_filter, key, visible, filterable="default" ): GridColumn.__init__( self, col_name, key=key, visible=visible, filterable=filterable) self.cols_to_filter = cols_to_filter @@ -432,6 +433,86 @@ complete_filter = or_( *clause_list ) return query.filter( complete_filter ) + +class OwnerColumn( TextColumn ): + """ Column that lists item's owner. """ + def get_value( self, trans, grid, item ): + return item.user.username + +class PublicURLColumn( TextColumn ): + """ Column displays item's public URL based on username and slug. """ + def get_link( self, trans, grid, item ): + if item.user.username and item.slug: + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + elif not item.user.username: + # TODO: provide link to set username. + return None + elif not item.user.slug: + # TODO: provide link to set slg + return None + +class DeletedColumn( GridColumn ): + """ Column that tracks and filters for items with deleted attribute. """ + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters + +class SharingStatusColumn( GridColumn ): + """ Grid column to indicate sharing status. """ + def get_value( self, trans, grid, item ): + # Delete items cannot be shared. + if item.deleted: + return "" + + # Build a list of sharing for this item. + sharing_statuses = [] + if item.users_shared_with: + sharing_statuses.append( "Shared" ) + if item.importable: + sharing_statuses.append( "Accessible" ) + if item.published: + sharing_statuses.append( "Published" ) + return ", ".join( sharing_statuses ) + + def get_link( self, trans, grid, item ): + if not item.deleted and ( item.users_shared_with or item.importable or item.published ): + return dict( operation="share or publish", id=item.id ) + return None + + def filter( self, db_session, user, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( self.model_class.users_shared_with == None ) + query = query.filter( self.model_class.importable == False ) + elif column_filter == "shared": + query = query.filter( self.model_class.users_shared_with != None ) + elif column_filter == "accessible": + query = query.filter( self.model_class.importable == True ) + elif column_filter == "published": + query = query.filter( self.model_class.published == True ) + return query + + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["accessible"] = "accessible" + accepted_filter_labels_and_vals["published"] = "published" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False, confirm=None ):

1 0

[hg] galaxy 3352: Bug fixes to slug editing, tooltips, and click...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/aa81684b9275 changeset: 3352:aa81684b9275 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 08 09:03:07 2010 -0500 description: Bug fixes to slug editing, tooltips, and click-to-edit elements. diffstat: lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/page.py | 2 +- lib/galaxy/web/controllers/workflow.py | 2 +- static/june_2007_style/base.css.tmpl | 6 +++--- static/june_2007_style/blue/base.css | 4 ++-- static/scripts/autocomplete_tagging.js | 9 +++++++-- static/scripts/galaxy.base.js | 7 +++++++ static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/trackster.js | 2 +- templates/root/history.mako | 6 +++--- templates/sharing_base.mako | 2 +- templates/tagging_common.mako | 26 ++++++++++++-------------- 13 files changed, 41 insertions(+), 31 deletions(-) diffs (246 lines): diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500 @@ -405,7 +405,7 @@ if history: history.slug = new_slug trans.sa_session.flush() - return + return history.slug @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500 @@ -547,7 +547,7 @@ if page: page.slug = new_slug trans.sa_session.flush() - return + return page.slug @web.expose @web.json diff -r 60308825b252 -r aa81684b9275 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Fri Feb 05 23:03:03 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500 @@ -389,7 +389,7 @@ if stored: stored.slug = new_slug trans.sa_session.flush() - return + return stored.slug @web.expose @web.json diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Feb 05 23:03:03 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Feb 08 09:03:07 2010 -0500 @@ -718,7 +718,7 @@ cursor: pointer; } -.tooltip span.tip { +span.tip { display: none } @@ -726,8 +726,8 @@ font-size: 90%; display: block; position: absolute; - right:2em;top:-1.75em; - width: inherit; + left:2em; + bottom:1.75em; background-color: black; color: white; text-align: center; diff -r 60308825b252 -r aa81684b9275 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Feb 05 23:03:03 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Feb 08 09:03:07 2010 -0500 @@ -120,7 +120,7 @@ .icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} .icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} .tooltip {position: relative; cursor: pointer} -.tooltip span.tip{display: none;} -.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;right:2em;top:-1.75em; width: inherit; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} +span.tip{display: none;} +.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;left:3em;bottom:1.75em; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} .editable-text{cursor:pointer} .editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right} \ No newline at end of file diff -r 60308825b252 -r aa81684b9275 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500 @@ -259,6 +259,7 @@ add_tag_button.show(); tag_input_field.hide(); tag_area.removeClass("active-tag-area"); + tag_area.addClass("tooltip"); } else { @@ -273,11 +274,14 @@ // If a "delete image" object was pressed and area is inactive, do nothing. if ($(e.target).hasClass("delete-tag-img") && !is_active) - return false; + return false; // If a "tag name" object was pressed and area is inactive, do nothing. if ($(e.target).hasClass("tag-name") && !is_active) - return false; + return false; + + // Remove tooltip. + $(this).removeClass("tooltip"); // Hide add tag button, show tag_input field. Change background to show // area is active. @@ -299,6 +303,7 @@ { tag_area.blur(); $(document).unbind("click", handle_document_click); + $(this).addClass("tooltip"); } }; // TODO: we should attach the click handler to all frames in order to capture diff -r 60308825b252 -r aa81684b9275 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/galaxy.base.js Mon Feb 08 09:03:07 2010 -0500 @@ -229,9 +229,13 @@ t.blur( function() { $(this).remove(); $("#" + text_elt_id).show(); + if (has_tooltip) + tooltip_elt.addClass("tooltip"); if (on_finish != null) on_finish(t); }); + var has_tooltip = $(this).hasClass("tooltip"); + var tooltip_elt = $(this); t.keyup( function( e ) { if ( e.keyCode == 27 ) { // Escape key @@ -268,6 +272,9 @@ t.insertAfter( $("#" + text_elt_id) ); t.focus(); t.select(); + + // Remove tooltip so that it doesn't show during editing. + $(this).removeClass("tooltip"); return false; }); diff -r 60308825b252 -r aa81684b9275 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Fri Feb 05 23:03:03 2010 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Mon Feb 08 09:03:07 2010 -0500 @@ -1,1 +1,1 @@ -function init_tag_click_function(b,a){$(b).find(".tag-name").each(function(){$(this).click(function(){var d=$(this).text();var c=d.split(":");a(c[0],c[1]);return true})})}jQuery.fn.autocomplete_tagging=function(q){var g={get_toggle_link_text_fn:function(r){var t="";var s=o(r);if(s!=0){t=s+(s!=0?" 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2010 -0500 +++ b/static/scripts/packed/trackster.js Mon Feb 08 09:03:07 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",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=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/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="../images/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="../images/visualization/strand_left_inv.png";left_i mg_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.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(c,a,b){this.chrom=c;this.config=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},remove_track:function(a){delete this .tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.lo w<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this .content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}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){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)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.widt h(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{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");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.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;var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.he ight_px+55+"px"});e.prependTo(a.container_div);a.draw()}}}})},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;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(!this.vertical_range){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f }}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#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);$("#linetrack_"+c+"_maxval").text(this.prefs.max_val ue);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;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=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dat aset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="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.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end -d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined ){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.vie w.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P); p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=func tion(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.lengt h;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/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="../images/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="../images/visualization/strand_left_inv.png";left_i mg_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.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(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},add_label_track:function (a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){delete this.tracks[a]},update_options:function(){for(var b in view.tracks){var a=view.tracks[b];if(a.update_options){a.update_options(b)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){f or(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.v iew.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}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){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)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{i nit:function(){this.data_queue={};this.data_cache=new Cache(CACHED_DATA);var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{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");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d.min;a.prefs.max_value=d.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;if($("#linetrack_"+b +"_minval").length===0){var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)}a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top: 0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),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(i).append(d).append(c)},update_options:function(c){var a=$("#trac k_"+c+"_minval").val(),b=$("#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(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20);this.prefs={block_color:"black",l abel_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.adClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.get JSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(thi s.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slo ts[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e =$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0 ).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 60308825b252 -r aa81684b9275 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/root/history.mako Mon Feb 08 09:03:07 2010 -0500 @@ -43,7 +43,7 @@ })); // Rename management. - async_save_text("history-name", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); + async_save_text("history-name-container", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); // Tag management. $('#history-tag').click( function() @@ -57,7 +57,7 @@ $('#history-annotation-area').toggle("fast"); return false; }); - async_save_text("history-annotation", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); + async_save_text("history-annotation-container", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); // Updater updater({ @@ -322,7 +322,7 @@ ## Annotation elt. <div id="history-annotation-area" class="form-row" style="display: none"> <label>Annotation / Notes:</label> - <div class="tooltip"> + <div id="history-annotation-container" class="tooltip"> %if annotation: <span id="history-annotation">${annotation | h}</span> %else: diff -r 60308825b252 -r aa81684b9275 templates/sharing_base.mako --- a/templates/sharing_base.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/sharing_base.mako Mon Feb 08 09:03:07 2010 -0500 @@ -49,7 +49,7 @@ }; <% controller_name = get_controller_name( item ) %> - async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", false, 0, on_start, on_finish); + async_save_text("edit-identifier", "item-identifier", "${h.url_for( controller=controller_name, action='set_slug_async', id=trans.security.encode_id( item.id ) )}", "new_slug", null, false, 0, on_start, on_finish); }); </script> </%def> diff -r 60308825b252 -r aa81684b9275 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Feb 05 23:03:03 2010 -0500 +++ b/templates/tagging_common.mako Mon Feb 08 09:03:07 2010 -0500 @@ -37,7 +37,7 @@ %if use_toggle_link: <a class="toggle-link" href="#">${num_tags} Tag${iff( num_tags == 1, "", "s")}</a> %endif - <div class="tag-area + <div class="tag-area tooltip %if tag_type == 'individual': individual-tag-area %endif @@ -72,20 +72,18 @@ %endfor ## Add tag input field. If element is in form, tag input is a textarea; otherwise element is a input type=text. - <div class="tooltip"> - %if editable: - %if in_form: - <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> - %else: - <input class="tag-input" type='text' size='${input_size}'/> - %endif - ## Add "add tag" button. - %if render_add_tag_button: - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> - %endif + %if editable: + %if in_form: + <textarea class="tag-input" rows='1' cols='${input_size}'></textarea> + %else: + <input class="tag-input" type='text' size='${input_size}'/> %endif - <span class="tip">Click to add tags</span> - </div> + ## Add "add tag" button. + %if render_add_tag_button: + <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + %endif + <span class="tip">Click to edit tags</span> + %endif </div> </div> </%def>

1 0

[hg] galaxy 3351: python2.4 sha.new() cannot be based to hmac - ...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/60308825b252 changeset: 3351:60308825b252 user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Fri Feb 05 23:03:03 2010 -0500 description: python2.4 sha.new() cannot be based to hmac - this patch tested with 2.4 and 2.5 diffstat: lib/galaxy/util/hash_util.py | 11 ++++++----- 1 files changed, 6 insertions(+), 5 deletions(-) diffs (30 lines): diff -r 4af74d038535 -r 60308825b252 lib/galaxy/util/hash_util.py --- a/lib/galaxy/util/hash_util.py Fri Feb 05 19:35:52 2010 -0500 +++ b/lib/galaxy/util/hash_util.py Fri Feb 05 23:03:03 2010 -0500 @@ -6,15 +6,16 @@ import sys, logging # Use hashlib module if for Python 2.5+, fall back on old sha and md5 modules +# sha1 requires explicit calls to new if also being passed to hmac (!) try: import hashlib sha1 = hashlib.sha1 + sha = sha1 md5 = hashlib.md5 except ImportError, e: - import sha, md5 - sha1 = sha.new - md5 = md5.new - + from sha import new as sha1 + import sha + from md5 import new as md5 import hmac log = logging.getLogger( __name__ ) @@ -30,4 +31,4 @@ return sha1() def hmac_new( key, value ): - return hmac.new( key, value, sha1 ).hexdigest() + return hmac.new( key, value, sha ).hexdigest()

1 0

[hg] galaxy 3350: typo
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4af74d038535 changeset: 3350:4af74d038535 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 05 19:35:52 2010 -0500 description: typo diffstat: lib/galaxy/web/controllers/tracks.py | 6 +++++- 1 files changed, 5 insertions(+), 1 deletions(-) diffs (16 lines): diff -r 432a32ba55bb -r 4af74d038535 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:35:52 2010 -0500 @@ -121,7 +121,11 @@ latest_revision = vis.latest_revision tracks = [] - dbkey = latest_revision.config['dbkey'] + try: + dbkey = latest_revision.config['dbkey'] + except KeyError: + dbkey = None + hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id']

1 0

[hg] galaxy 3349: trackster:
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/432a32ba55bb changeset: 3349:432a32ba55bb user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 05 19:08:37 2010 -0500 description: trackster: - New interface for new track browsers - Saving shows progress bar - Can now add tracks async - Switching dbkeys is now async diffstat: lib/galaxy/web/controllers/tracks.py | 128 ++++------ lib/galaxy/web/controllers/visualization.py | 2 +- static/scripts/trackster.js | 61 +++- static/trackster.css | 1 + templates/grid_base.mako | 4 + templates/tracks/add_tracks.mako | 3 +- templates/tracks/browser.mako | 344 ++++++++++++++++----------- templates/tracks/index.mako | 52 +++- templates/tracks/new_browser.mako | 81 +----- 9 files changed, 359 insertions(+), 317 deletions(-) diffs (955 lines): diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Feb 05 16:34:30 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 05 19:08:37 2010 -0500 @@ -57,10 +57,7 @@ use_paging = False columns = [ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), - # grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Filetype", key="extension" ), - # Columns that are valid for filtering but are not visible. - # SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" ) ] def apply_default_filter( self, trans, query, **kwargs ): if self.available_tracks is None: @@ -80,62 +77,40 @@ @web.expose def index( self, trans ): - return trans.fill_template( "tracks/index.mako" ) - + config = {} + + return trans.fill_template( "tracks/browser.mako", config=config ) + @web.expose @web.require_login() - def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ): - """ - Build a new browser from datasets in the current history. Redirects - to 'browser' once datasets to browse have been selected. - """ - session = trans.sa_session - # If the user clicked the submit button explicitly, try to build the browser - if title and browse and dataset_ids: - if not isinstance( dataset_ids, list ): - dataset_ids = [ dataset_ids ] - # Build config - tracks = [] - for dataset_id in dataset_ids: - tracks.append( { "dataset_id": str( dataset_id ) } ) - config = { "tracks": tracks } - # Build visualization object - vis = model.Visualization() - vis.user = trans.user - vis.title = title - vis.type = "trackster" - vis_rev = model.VisualizationRevision() - vis_rev.visualization = vis - vis_rev.title = title - vis_rev.config = config - vis.latest_revision = vis_rev - session.add( vis ) - session.add( vis_rev ) - session.flush() - trans.response.send_redirect( web.url_for( controller='tracks', action='browser', id=trans.security.encode_id( vis.id ) ) ) + def new_browser( self, trans ): + dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] + dbkey_set = set( dbkeys ) + if not dbkey_set: + return trans.show_error_message( "Current history has no valid datasets to visualize." ) else: - # Determine the set of all dbkeys that are used in the current history - dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] - dbkey_set = set( dbkeys ) - if not dbkey_set: - return trans.show_error_message( "Current history has no valid datasets to visualize." ) - - # If a dbkey argument was not provided, or is no longer valid, default - # to the first one - if dbkey is None or dbkey not in dbkey_set: - dbkey = dbkeys[0] - # Find all datasets in the current history that are of that dbkey - # and can be displayed - datasets = {} - if self.available_tracks is None: - self.available_tracks = trans.app.datatypes_registry.get_available_tracks() - for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and dataset.extension in self.available_tracks: - datasets[dataset.id] = (dataset.extension, dataset.name) - # Render the template - return trans.fill_template( "tracks/new_browser.mako", available_tracks=self.available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) - + return trans.fill_template( "tracks/new_browser.mako", dbkey_set=dbkey_set ) + + @web.json + @web.require_login() + def add_track_async(self, trans, id): + dataset_id = trans.security.decode_id( id ) + + hda_query = trans.sa_session.query( model.HistoryDatasetAssociation ) + dataset = hda_query.get( dataset_id ) + track_type, indexer = dataset.datatype.get_track_type() + + track = { + "track_type": track_type, + "indexer": indexer, + "name": dataset.name, + "dataset_id": dataset.id, + "prefs": {}, + } + return track + @web.expose + @web.require_login() def browser(self, trans, id, chrom=""): """ Display browser for the datasets listed in `dataset_ids`. @@ -143,8 +118,10 @@ decoded_id = trans.security.decode_id( id ) session = trans.sa_session vis = session.query( model.Visualization ).get( decoded_id ) + latest_revision = vis.latest_revision tracks = [] - dbkey = "" + + dbkey = latest_revision.config['dbkey'] hda_query = session.query( model.HistoryDatasetAssociation ) for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] @@ -161,18 +138,10 @@ "dataset_id": dataset.id, "prefs": simplejson.dumps(prefs), } ) - dbkey = dataset.dbkey - chrom_lengths = self._chroms( trans, dbkey ) - if chrom_lengths is None: - error( "No chromosome lengths file found for '%s'" % dataset.name ) - return trans.fill_template( 'tracks/browser.mako', - #dataset_ids=dataset_ids, - title = vis.title, - id=id, - tracks=tracks, - chrom=chrom, - dbkey=dbkey, - LEN=chrom_lengths.get(chrom, 0) ) + if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat + + config = { "title": vis.title, "vis_id": id, "tracks": tracks, "chrom": chrom, "dbkey": dbkey } + return trans.fill_template( 'tracks/browser.mako', config=config ) @web.json def chroms(self, trans, dbkey=None ): @@ -288,9 +257,19 @@ @web.json def save( self, trans, **kwargs ): - decoded_id = trans.security.decode_id( kwargs['id'] ) session = trans.sa_session - vis = session.query( model.Visualization ).get( decoded_id ) + vis_id = kwargs['vis_id'].strip('"') + dbkey = kwargs['dbkey'] + + if vis_id == "undefined": # new vis + vis = model.Visualization() + vis.user = trans.user + vis.title = kwargs['vis_title'] + vis.type = "trackster" + session.add( vis ) + else: + decoded_id = trans.security.decode_id( vis_id ) + vis = session.query( model.Visualization ).get( decoded_id ) decoded_payload = simplejson.loads( kwargs['payload'] ) vis_rev = model.VisualizationRevision() @@ -304,10 +283,11 @@ "track_type": track['track_type'], "prefs": track['prefs'] } ) - vis_rev.config = { "tracks": tracks } + vis_rev.config = { "dbkey": dbkey, "tracks": tracks } vis.latest_revision = vis_rev session.add( vis_rev ) session.flush() + return trans.security.encode_id(vis.id) data_grid = DatasetSelectionGrid() @@ -316,11 +296,5 @@ def list_datasets( self, trans, **kwargs ): """List all datasets that can be added as tracks""" - # Render the list view - # return trans.fill_template( 'tracks/add_tracks.mako', grid=data_grid( trans, status=status, message=message, **kwargs ) ) return self.data_grid( trans, **kwargs ) - - # - - \ No newline at end of file diff -r 99483ae6c738 -r 432a32ba55bb lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Fri Feb 05 16:34:30 2010 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Fri Feb 05 19:08:37 2010 -0500 @@ -7,7 +7,7 @@ # Grid definition title = "Visualizations" model_class = model.Visualization - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ grids.GridColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), diff -r 99483ae6c738 -r 432a32ba55bb static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Feb 05 16:34:30 2010 -0500 +++ b/static/scripts/trackster.js Fri Feb 05 19:08:37 2010 -0500 @@ -77,14 +77,16 @@ } }); -var View = function( chrom, max_high, config ) { +var View = function( chrom, title, vis_id, dbkey ) { + this.vis_id = vis_id; + this.dbkey = dbkey; + this.title = title; this.chrom = chrom; - this.config = config; this.tracks = []; + this.label_tracks = []; this.max_low = 0; - this.max_high = max_high; + this.max_high = 0; this.center = (this.max_high - this.max_low) / 2; - this.span = this.max_high - this.max_low; this.zoom_factor = 3; this.zoom_level = 0; }; @@ -94,6 +96,10 @@ this.tracks.push( track ); if (track.init) { track.init(); } }, + add_label_track: function ( label_track ) { + label_track.view = this; + this.label_tracks.push( label_track ); + }, remove_track: function( track ) { delete this.tracks[track]; }, @@ -105,7 +111,8 @@ } } }, - redraw: function() { + redraw: function(nodraw) { + this.span = this.max_high - this.max_low; var span = this.span / Math.pow(this.zoom_factor, this.zoom_level), low = this.center - (span / 2), high = low + span; @@ -134,11 +141,14 @@ }).show(); $("#low").val( commatize(this.low) ); $("#high").val( commatize(this.high) ); - for ( var i = 0, len = this.tracks.length; i < len; i++ ) { - this.tracks[i].draw(); + if (!nodraw) { + for ( var i = 0, len = this.tracks.length; i < len; i++ ) { + this.tracks[i].draw(); + } + for ( var i = 0, len = this.label_tracks.length; i < len; i++ ) { + this.label_tracks[i].draw(); + } } - //$("#bottom-spacer").remove(); - //$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>'); }, zoom_in: function ( point ) { if (this.max_high === 0 || this.high - this.low < 30) { @@ -238,6 +248,7 @@ var LabelTrack = function ( parent_element ) { Track.call( this, null, parent_element ); + this.track_type = "LabelTrack"; this.hidden = true; this.container_div.addClass( "label-track" ); }; @@ -273,26 +284,27 @@ this.height_px = 100; this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; - this.data_queue = {}; - this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of - // asynchronous calls this.prefs = { 'min_value': undefined, 'max_value': undefined }; if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { + this.data_queue = {}; + this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of + // asynchronous calls var track = this, track_id = track.view.tracks.indexOf(track); - + track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); $.getJSON( data_url, { stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { track.container_div.addClass("error"); track.content_div.text(DATA_ERROR); - } else if (data == "no data") { + } else if (data.length === 0 || data == "no data") { track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (data == "pending") { @@ -313,15 +325,17 @@ } track.vertical_range = track.prefs.max_value - track.prefs.min_value; - // Draw y-axis labels - var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); - var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); + // Draw y-axis labels if necessary + if ( $('#linetrack_' + track_id + '_minval').length === 0) { + var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); - max_label.css({ position: "relative", top: "25px" }); - max_label.prependTo(track.container_div); + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); - min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); - min_label.prependTo(track.container_div); + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); + min_label.prependTo(track.container_div); + } track.draw(); } @@ -345,7 +359,7 @@ } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - if (!this.vertical_range) { // We don't have the necessary information yet + if (this.vertical_range === undefined) { // We don't have the necessary information yet return; } @@ -463,6 +477,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { @@ -473,7 +488,7 @@ track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (data == "pending") { - track.container_div.addClass("pending"); + track.container_div.adClass("pending"); track.content_div.text(DATA_PENDING); setTimeout(function() { track.init(); }, 5000); } else { diff -r 99483ae6c738 -r 432a32ba55bb static/trackster.css --- a/static/trackster.css Fri Feb 05 16:34:30 2010 -0500 +++ b/static/trackster.css Fri Feb 05 19:08:37 2010 -0500 @@ -8,6 +8,7 @@ #nav-container { position: fixed; + left: 0; bottom: 0; } diff -r 99483ae6c738 -r 432a32ba55bb templates/grid_base.mako --- a/templates/grid_base.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/grid_base.mako Fri Feb 05 19:08:37 2010 -0500 @@ -27,6 +27,10 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${self.grid_javascripts()} +</%def> + +<%def name="grid_javascripts()"> ${h.js("jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> ## TODO: generalize and move into galaxy.base.js diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/add_tracks.mako --- a/templates/tracks/add_tracks.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/add_tracks.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,8 +1,9 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> -${javascripts()} ${stylesheets()} +${grid_javascripts()} + ${render_grid_table( grid, show_item_checkboxes=True )} ## Initialize the grid. diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/browser.mako Fri Feb 05 19:08:37 2010 -0500 @@ -45,7 +45,7 @@ </div> </div> -<div id="nav-container"> +<div id="nav-container" style="width:100%;"> <div id="nav-labeltrack"></div> <div id="nav"> <div id="overview"> @@ -59,8 +59,7 @@ <option value="">Loading</option> </select> <input id="low" size="12" />:<input id="high" size="12" /> - ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" /> - <input type="hidden" name="id" value="${id}" /> + <input type="hidden" name="id" value="${config.get('vis_id', '')}" /> <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> @@ -75,11 +74,10 @@ <div class="unified-panel-header-inner">Configuration</div> </div> <form action="${h.url_for( action='update_config' )}"> -## <input name="title" id="title" value="${title}" /> +## <input name="title" id="title" value="${config.title}" /> <div id="show-hide-move"> <ul id="sortable-ul"></ul> </div> -## <input type="submit" id="update-config" value="Save settings" /> <input type="button" id="refresh-button" value="Refresh" /> <input type="button" id="save-button" value="Save" /> <input id="add-track" type="button" value="Add Track" /> @@ -89,154 +87,227 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} +${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} <script type="text/javascript"> var data_url = "${h.url_for( action='data' )}"; - var view = new View( "${chrom}", ${LEN} ); + var view; $(function() { - view.add_track( new LabelTrack( $("#top-labeltrack" ) ) ); - view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); - - %for track in tracks: - view.add_track( - new ${track["track_type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} ) - ); - %endfor - - $(document).bind( "redraw", function( e ) { - view.redraw(); - }); - - $("#content").bind("mousewheel", function( e, delta ) { - if (delta > 0) { - view.zoom_in(e.pageX); - } else { - view.zoom_out(); - } - e.preventDefault(); - }); - - $("#content").bind("dblclick", function( e ) { - view.zoom_in(e.pageX); - }); - - // To let the overview box be draggable - $("#overview-box").bind("dragstart", function( e ) { - this.current_x = e.offsetX; - }).bind("drag", function( e ) { - var delta = e.offsetX - this.current_x; - this.current_x = e.offsetX; - - var delta_chrom = Math.round(delta / $(document).width() * view.span); - view.center += delta_chrom; - view.redraw(); - }); - - // To adjust the size of the viewport to fit the fixed-height footer - var refresh = function( e ) { - $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); - $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); - $("#nav-container").width( $("#center").width() ); - view.redraw(); - }; - $(window).bind( "resize", function(e) { refresh(e); } ); - $("#right-border").bind( "click", function(e) { refresh(e); } ); - $("#right-border").bind( "dragend", function(e) { refresh(e); } ); - $(window).trigger( "resize" ); - - $("#viewport").bind( "dragstart", function( e ) { - this.original_low = view.low; - this.current_height = e.clientY; - this.current_x = e.offsetX; - }).bind( "drag", function( e ) { - var container = $(this).parent(); - var delta = e.offsetX - this.current_x; - var new_scroll = container.scrollTop() - (e.clientY - this.current_height); - if ( new_scroll < container.get(0).scrollHeight - container.height() ) { - container.scrollTop(new_scroll); - } - this.current_height = e.clientY; - this.current_x = e.offsetX; - - var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); - view.center -= delta_chrom; - view.redraw(); - }); - - $("#refresh-button").bind( "click", function(e) { - view.update_options(); - }); - - // Use a popup grid to add more tracks - $("#add-track").bind( "click", function(e) { + %if config: + view = new View( "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + %for track in config.get('tracks'): + view.add_track( + new ${track["track_type"]}( "${track['name'] | h}", ${track['dataset_id']}, "${track['indexer']}", ${track['prefs']} ) + ); + %endfor + init(); + %else: $.ajax({ - url: "${h.url_for( action='list_datasets' )}", + url: "${h.url_for( action='new_browser' )}", data: {}, - error: function() { alert( "Grid refresh failed" ) }, - success: function(table_html) { - show_modal("Add Track — Select Dataset(s)", table_html, { - "Insert": function() { - hide_modal(); - }, - "Cancel": function() { + error: function() { alert( "Couldn't create new browser" ) }, + success: function(form_html) { + show_modal("New Track Browser", form_html, { + "Continue": function() { + view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() ); + init(); hide_modal(); } }); } }); - }); + %endif - $("#save-button").bind("click", function(e) { - view.update_options(); - var sorted = $("ul#sortable-ul").sortable('toArray'); - var payload = []; - for (var i in sorted) { - var track_id = parseInt(sorted[i].split("track_")[1]), - track = view.tracks[track_id]; - - payload.push( { - "track_type": track.track_type, - "indexer": track.indexer, - "name": track.name, - "dataset_id": track.dataset_id, - "prefs": track.prefs - }); - } - $.ajax({ - url: "${h.url_for( action='save' )}", - data: { - 'id': '${id}', - 'payload': JSON.stringify(payload) + // Execute this when everything is ready + function init() { + $("ul#sortable-ul").sortable({ + update: function(event, ui) { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + } } }); - }); - - // Execute this on page load - (function () { - $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: "${dbkey}" }, function ( data ) { + + $(document).bind( "redraw", function( e ) { + view.redraw(); + }); + + $("#content").bind("mousewheel", function( e, delta ) { + if (delta > 0) { + view.zoom_in(e.pageX); + } else { + view.zoom_out(); + } + e.preventDefault(); + }); + + $("#content").bind("dblclick", function( e ) { + view.zoom_in(e.pageX); + }); + + // To let the overview box be draggable + $("#overview-box").bind("dragstart", function( e ) { + this.current_x = e.offsetX; + }).bind("drag", function( e ) { + var delta = e.offsetX - this.current_x; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * view.span); + view.center += delta_chrom; + view.redraw(); + }); + + // To adjust the size of the viewport to fit the fixed-height footer + var refresh = function( e ) { + $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); + $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); + $("#nav-container").width( $("#center").width() ); + view.redraw(); + }; + $(window).bind( "resize", function(e) { refresh(e); } ); + $("#right-border").bind( "click", function(e) { refresh(e); } ); + $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $(window).trigger( "resize" ); + + $("#viewport").bind( "dragstart", function( e ) { + this.original_low = view.low; + this.current_height = e.clientY; + this.current_x = e.offsetX; + }).bind( "drag", function( e ) { + var container = $(this).parent(); + var delta = e.offsetX - this.current_x; + var new_scroll = container.scrollTop() - (e.clientY - this.current_height); + if ( new_scroll < container.get(0).scrollHeight - container.height() ) { + container.scrollTop(new_scroll); + } + this.current_height = e.clientY; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); + view.center -= delta_chrom; + view.redraw(); + }); + + $("#refresh-button").bind( "click", function(e) { + view.update_options(); + }); + + // Use a popup grid to add more tracks + $("#add-track").bind( "click", function(e) { + $.ajax({ + url: "${h.url_for( action='list_datasets' )}", + data: {}, + error: function() { alert( "Grid refresh failed" ) }, + success: function(table_html) { + show_modal("Add Track — Select Dataset(s)", table_html, { + "Insert": function() { + $('input[name=id]:checked').each(function() { + var item_id = $(this).val(); + $.ajax( { + url: "${h.url_for( action='add_track_async' )}", + data: { id: item_id }, + dataType: "json", + error: function() {}, + success: function(track_data) { + var new_track; + var td = track_data; + switch(track_data.track_type) { + case "LineTrack": + new_track = new LineTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + case "FeatureTrack": + new_track = new FeatureTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + case "ReadTrack": + new_track = new ReadTrack( track_data.name, track_data.dataset_id, track_data.indexer, track_data.prefs ); + break; + } + view.add_track(new_track); + sidebar_box(new_track); + } + }); + + }); + + hide_modal(); + }, + "Cancel": function() { + hide_modal(); + } + }); + } + }); + }); + + $("#save-button").bind("click", function(e) { + view.update_options(); + var sorted = $("ul#sortable-ul").sortable('toArray'); + var payload = []; + for (var i in sorted) { + var track_id = parseInt(sorted[i].split("track_")[1]), + track = view.tracks[track_id]; + + payload.push( { + "track_type": track.track_type, + "indexer": track.indexer, + "name": track.name, + "dataset_id": track.dataset_id, + "prefs": track.prefs + }); + } + // Show saving dialog box + show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); + + $.ajax({ + url: "${h.url_for( action='save' )}", + data: { + 'vis_id': view.vis_id, + 'vis_title': view.title, + 'dbkey': view.dbkey, + 'payload': JSON.stringify(payload) + }, + success: function(vis_id) { + view.vis_id = vis_id; + hide_modal(); + } + }); + }); + + view.add_label_track( new LabelTrack( $("#top-labeltrack" ) ) ); + view.add_label_track( new LabelTrack( $("#nav-labeltrack" ) ) ); + + $.getJSON( "${h.url_for( action='chroms' )}", { dbkey: view.dbkey }, function ( data ) { + view.chrom_data = data; var chrom_options = '<option value="">Select Chrom/Contig</option>'; for (i in data) { - chrom = data[i]['chrom'] - if( chrom == view.chrom ) { - chrom_options += '<option value="' + chrom + '" selected="true">' + chrom + '</option>'; - } else { - chrom_options += '<option value="' + chrom + '">' + chrom + '</option>'; - } + var chrom = data[i]['chrom'] + chrom_options += '<option value="' + chrom + '">' + chrom + '</option>'; } $("#chrom").html(chrom_options); $("#chrom").bind( "change", function () { - $("#chr").submit(); + view.chrom = $("#chrom").val(); + var found = $.grep(view.chrom_data, function(v, i) { + return v.chrom === view.chrom; + })[0]; + view.max_high = found.len; + view.redraw(true); + + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (track.init) { + track.init(); + } + } + // view.redraw(); }); }); - // Populate sort/move ul - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; + function sidebar_box(track) { if (!track.hidden) { + var track_id = view.tracks.length -1; // Track was just added to view, so index is current length -1 var label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'); var title = $('<div class="historyItemTitle"></div>'); var del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'); @@ -255,18 +326,17 @@ li.append(div); $("ul#sortable-ul").append(li); } + }; + + // Populate sort/move ul + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + sidebar_box(track); } - $("ul#sortable-ul").sortable({ - update: function(event, ui) { - for (var track_id in view.tracks) { - var track = view.tracks[track_id]; - } - } - }); - - })(); - $(window).trigger("resize"); + $(window).trigger("resize"); + }; + }); </script> diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/index.mako --- a/templates/tracks/index.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/index.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,16 +1,38 @@ -<%inherit file="/base_panels.mako"/> +<form id="form" method="POST"> + <div class="form-row"> + <label for="dbkey">Browser name:</label> + <div class="form-row-input"> + <input type="text" name="title" id="title" value="Unnamed Browser"></input> + </div> + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <label for="dbkey">Reference genome build (dbkey): </label> + <div class="form-row-input"> + <select name="dbkey" id="dbkey" refresh_on_change="true"> + %for tmp_dbkey in dbkey_set: + <option value="${tmp_dbkey}" + %if tmp_dbkey == dbkey: + selected="selected" + %endif + >${tmp_dbkey}</option> + %endfor + </select> + </div> + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> + %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): + <div> + <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> + <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> + </div> + %endfor -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="visualization" - self.message_box_visible=False -%> -</%def> - -<%def name="center_panel()"> - - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="tracks", action="new_browser" )}"> </iframe> - -</%def> \ No newline at end of file + <div style="clear: both;"></div> + </div> + <div class="form-row"> + <input type="submit" name="browse" value="Browse"/> + </div> +</form> diff -r 99483ae6c738 -r 432a32ba55bb templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Fri Feb 05 16:34:30 2010 -0500 +++ b/templates/tracks/new_browser.mako Fri Feb 05 19:08:37 2010 -0500 @@ -1,65 +1,20 @@ -<%inherit file="/base.mako"/> - -<%def name="javascripts()"> -${parent.javascripts()} -<script type="text/javascript"> -$( function() { - $( "select[refresh_on_change='true']").change( function() { - $("#form").submit(); - }); -}); -</script> -</%def> - -% if not available_tracks: - <div class="errormessagelarge"> - There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains - converters for datatypes (see tool_conf.xml.sample) for examples. +<form id="form" method="POST"> + <div class="form-row"> + <label for="title">Browser name:</label> + <div class="form-row-input"> + <input type="text" name="title" id="new-title" value="Unnamed Browser"></input> + </div> + <div style="clear: both;"></div> </div> - -% else: - <div class="form"> - <div class="form-title">Create new track browser</div> - - <div id="dbkey" class="form-body"> - <form id="form" method="POST"> - <div class="form-row"> - <label for="dbkey">Browser name:</label> - <div class="form-row-input"> - <input type="text" name="title" id="title" value="Unnamed Browser"></input> - </div> - <div style="clear: both;"></div> - </div> - <div class="form-row"> - <label for="dbkey">Reference genome build (dbkey): </label> - <div class="form-row-input"> - <select name="dbkey" id="dbkey" refresh_on_change="true"> - %for tmp_dbkey in dbkey_set: - <option value="${tmp_dbkey}" - %if tmp_dbkey == dbkey: - selected="selected" - %endif - >${tmp_dbkey}</option> - %endfor - </select> - </div> - <div style="clear: both;"></div> - </div> - <div class="form-row"> - <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> - %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): - <div> - <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> - <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> - </div> - %endfor - - <div style="clear: both;"></div> - </div> - </div> - <div class="form-row"> - <input type="submit" name="browse" value="Browse"/> - </div> - </form> + <div class="form-row"> + <label for="dbkey">Reference genome build (dbkey): </label> + <div class="form-row-input"> + <select name="dbkey" id="new-dbkey"> + %for dbkey in dbkey_set: + <option value="${dbkey}">${dbkey}</option> + %endfor + </select> + </div> + <div style="clear: both;"></div> </div> -% endif +</form>

1 0

[hg] galaxy 3348: Prevent history tag and annotation icons from ...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/99483ae6c738 changeset: 3348:99483ae6c738 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 05 16:34:30 2010 -0500 description: Prevent history tag and annotation icons from wrapping. diffstat: templates/root/history.mako | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r 656e1014f2fa -r 99483ae6c738 templates/root/history.mako --- a/templates/root/history.mako Fri Feb 05 16:27:18 2010 -0500 +++ b/templates/root/history.mako Fri Feb 05 16:34:30 2010 -0500 @@ -286,8 +286,8 @@ <span class="tip">Click to edit</span></a> </div> </td> - <td align="right"> - <div style="float: right"> + <td align="right" style="width: 40px"> + <div style="float: right; white-space: nowrap"> <a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> <a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> </div>

1 0

[hg] galaxy 3347: Add a label for experiment name in MACs
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/656e1014f2fa changeset: 3347:656e1014f2fa user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 16:27:18 2010 -0500 description: Add a label for experiment name in MACs diffstat: tools/peak_calling/macs_wrapper.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r e9de35947c06 -r 656e1014f2fa tools/peak_calling/macs_wrapper.xml --- a/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:06:27 2010 -0500 +++ b/tools/peak_calling/macs_wrapper.xml Fri Feb 05 16:27:18 2010 -0500 @@ -6,7 +6,7 @@ <requirement type="binary">macs</requirement> </requirements> <inputs> - <param name="experiment_name" type="text" value="MACS in Galaxy" size="50"/> + <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/> <conditional name="input_type"> <param name="input_type_selector" type="select" label="Paired End Sequencing"> <option value="paired_end">Paired End (requires elandmultipet format)</option>

1 0

[hg] galaxy 3346: Create NGS peak calling section. Add MACS peak...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e9de35947c06 changeset: 3346:e9de35947c06 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Feb 05 16:06:27 2010 -0500 description: Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version. diffstat: test-data/chipseq_enriched.bed.gz | 0 test-data/chipseq_input.bed.gz | 0 test-data/macs_test_1_out.bed | 1271 ++++++++++++++++++++ test-data/macs_test_2_neg_peaks_out.interval | 59 + test-data/macs_test_2_peaks_out.interval | 1289 +++++++++++++++++++++ tool_conf.xml.main | 6 +- tool_conf.xml.sample | 7 +- tools/genetrack/genetrack_indexer.py | 42 + tools/genetrack/genetrack_indexer.xml | 54 + tools/genetrack/genetrack_peak_prediction.py | 40 + tools/genetrack/genetrack_peak_prediction.xml | 59 + tools/peak_calling/macs_wrapper.py | 138 ++ tools/peak_calling/macs_wrapper.xml | 213 +++ tools/samtools/sam2interval.xml | 2 +- tools/visualization/genetrack_indexer.py | 39 - tools/visualization/genetrack_indexer.xml | 54 - tools/visualization/genetrack_peak_prediction.py | 40 - tools/visualization/genetrack_peak_prediction.xml | 59 - 18 files changed, 3176 insertions(+), 196 deletions(-) diffs (truncated from 3460 to 3000 lines): diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_enriched.bed.gz Binary file test-data/chipseq_enriched.bed.gz has changed diff -r 49961332adb6 -r e9de35947c06 test-data/chipseq_input.bed.gz Binary file test-data/chipseq_input.bed.gz has changed diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_1_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_1_out.bed Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,1271 @@ +track name="MACS peaks for MACS_in_Galaxy" +chr1 3138857 3139271 MACS_peak_1 53.08 +chr1 4133899 4134700 MACS_peak_2 51.91 +chr1 4323670 4324367 MACS_peak_3 272.01 +chr1 4336486 4337946 MACS_peak_4 228.35 +chr1 4407086 4409120 MACS_peak_5 300.46 +chr1 4507832 4508710 MACS_peak_6 161.74 +chr1 4657704 4658572 MACS_peak_7 280.37 +chr1 4658705 4659021 MACS_peak_8 131.25 +chr1 4659147 4660581 MACS_peak_9 463.08 +chr1 4661156 4661317 MACS_peak_10 174.88 +chr1 4661505 4661617 MACS_peak_11 100.24 +chr1 4661790 4662463 MACS_peak_12 219.58 +chr1 4662710 4663434 MACS_peak_13 395.94 +chr1 4664135 4664430 MACS_peak_14 169.10 +chr1 4665001 4665113 MACS_peak_15 100.24 +chr1 4665839 4666425 MACS_peak_16 332.40 +chr1 4666581 4666693 MACS_peak_17 100.24 +chr1 4666840 4666981 MACS_peak_18 174.88 +chr1 4667600 4667712 MACS_peak_19 100.24 +chr1 4668711 4669005 MACS_peak_20 169.17 +chr1 4669126 4669238 MACS_peak_21 100.24 +chr1 4669537 4669752 MACS_peak_22 174.88 +chr1 4669936 4670048 MACS_peak_23 100.24 +chr1 4670216 4670449 MACS_peak_24 212.68 +chr1 4673856 4674051 MACS_peak_25 137.07 +chr1 4674349 4674478 MACS_peak_26 137.07 +chr1 4675027 4675152 MACS_peak_27 137.07 +chr1 4676227 4676339 MACS_peak_28 100.24 +chr1 4676511 4676623 MACS_peak_29 100.24 +chr1 4676954 4677151 MACS_peak_30 100.24 +chr1 4677646 4677758 MACS_peak_31 100.24 +chr1 4678360 4678472 MACS_peak_32 100.24 +chr1 4678659 4679136 MACS_peak_33 230.04 +chr1 4679439 4679551 MACS_peak_34 100.24 +chr1 4680106 4680523 MACS_peak_35 126.43 +chr1 4680822 4680934 MACS_peak_36 100.24 +chr1 4681075 4682050 MACS_peak_37 241.81 +chr1 4682229 4682387 MACS_peak_38 100.24 +chr1 4682594 4682706 MACS_peak_39 100.24 +chr1 4683158 4683270 MACS_peak_40 100.24 +chr1 4683473 4683585 MACS_peak_41 100.24 +chr1 4683832 4683944 MACS_peak_42 100.24 +chr1 4684591 4684775 MACS_peak_43 100.24 +chr1 4685292 4685404 MACS_peak_44 100.24 +chr1 4685810 4686198 MACS_peak_45 127.69 +chr1 4686493 4686605 MACS_peak_46 100.24 +chr1 4686818 4686930 MACS_peak_47 100.24 +chr1 4687387 4687499 MACS_peak_48 100.24 +chr1 4687692 4687902 MACS_peak_49 174.88 +chr1 4688181 4688790 MACS_peak_50 258.16 +chr1 4689101 4689557 MACS_peak_51 231.41 +chr1 4690039 4690151 MACS_peak_52 100.24 +chr1 4690290 4690402 MACS_peak_53 100.24 +chr1 4690780 4690907 MACS_peak_54 137.07 +chr1 4691478 4692335 MACS_peak_55 315.89 +chr1 4692464 4692768 MACS_peak_56 131.92 +chr1 4693243 4693751 MACS_peak_57 228.13 +chr1 4694306 4694418 MACS_peak_58 100.24 +chr1 4694738 4695016 MACS_peak_59 170.38 +chr1 4695207 4695378 MACS_peak_60 100.24 +chr1 4695503 4696600 MACS_peak_61 374.29 +chr1 4696903 4697015 MACS_peak_62 100.24 +chr1 4697569 4697912 MACS_peak_63 240.07 +chr1 4698224 4698395 MACS_peak_64 100.24 +chr1 4698790 4698904 MACS_peak_65 137.07 +chr1 4699223 4699430 MACS_peak_66 137.07 +chr1 4699642 4699754 MACS_peak_67 100.24 +chr1 4700457 4700569 MACS_peak_68 100.24 +chr1 4700853 4700965 MACS_peak_69 100.24 +chr1 4708474 4708898 MACS_peak_70 126.15 +chr1 4709426 4709741 MACS_peak_71 167.67 +chr1 4709925 4710127 MACS_peak_72 137.07 +chr1 4710465 4710577 MACS_peak_73 100.24 +chr1 4710812 4711277 MACS_peak_74 194.68 +chr1 4711462 4711762 MACS_peak_75 132.15 +chr1 4712202 4712479 MACS_peak_76 97.58 +chr1 4712673 4713163 MACS_peak_77 340.17 +chr1 4713659 4714656 MACS_peak_78 414.78 +chr1 4714840 4715470 MACS_peak_79 221.59 +chr1 4715671 4715783 MACS_peak_80 100.24 +chr1 4715908 4716811 MACS_peak_81 530.04 +chr1 4717318 4717430 MACS_peak_82 100.24 +chr1 4717789 4718230 MACS_peak_83 232.43 +chr1 4718990 4719236 MACS_peak_84 99.13 +chr1 4719718 4719830 MACS_peak_85 100.24 +chr1 4720276 4720388 MACS_peak_86 100.24 +chr1 4721061 4721173 MACS_peak_87 100.24 +chr1 4721620 4721782 MACS_peak_88 100.24 +chr1 4722229 4722341 MACS_peak_89 100.24 +chr1 4723262 4723374 MACS_peak_90 100.24 +chr1 4724496 4724608 MACS_peak_91 100.24 +chr1 4726179 4726291 MACS_peak_92 100.24 +chr1 4726472 4727091 MACS_peak_93 187.23 +chr1 4727268 4727705 MACS_peak_94 196.30 +chr1 4727871 4727983 MACS_peak_95 100.24 +chr1 4728976 4729088 MACS_peak_96 100.24 +chr1 4729473 4729611 MACS_peak_97 137.07 +chr1 4729954 4730093 MACS_peak_98 137.07 +chr1 4730636 4730805 MACS_peak_99 100.24 +chr1 4730936 4731305 MACS_peak_100 164.24 +chr1 4731799 4732585 MACS_peak_101 355.47 +chr1 4733192 4733304 MACS_peak_102 100.24 +chr1 4733710 4733831 MACS_peak_103 137.07 +chr1 4734062 4734891 MACS_peak_104 352.92 +chr1 4735075 4735290 MACS_peak_105 137.07 +chr1 4735523 4736190 MACS_peak_106 185.28 +chr1 4736399 4737184 MACS_peak_107 355.53 +chr1 4737395 4737601 MACS_peak_108 137.07 +chr1 4737973 4738425 MACS_peak_109 231.68 +chr1 4738796 4739212 MACS_peak_110 197.58 +chr1 4739379 4739491 MACS_peak_111 100.24 +chr1 4739612 4740720 MACS_peak_112 588.51 +chr1 4741405 4741655 MACS_peak_113 135.32 +chr1 4741998 4742300 MACS_peak_114 132.04 +chr1 4742829 4742952 MACS_peak_115 137.07 +chr1 4743079 4743327 MACS_peak_116 135.46 +chr1 4743612 4744566 MACS_peak_117 453.30 +chr1 4744719 4745224 MACS_peak_118 264.66 +chr1 4745398 4745786 MACS_peak_119 236.32 +chr1 4746034 4746316 MACS_peak_120 170.07 +chr1 4747206 4748408 MACS_peak_121 474.57 +chr1 4748814 4748926 MACS_peak_122 100.24 +chr1 4749222 4749334 MACS_peak_123 100.24 +chr1 4749686 4750054 MACS_peak_124 275.66 +chr1 4750335 4750697 MACS_peak_125 164.65 +chr1 4750863 4751682 MACS_peak_126 247.87 +chr1 4751853 4752428 MACS_peak_127 189.15 +chr1 4752581 4753611 MACS_peak_128 412.95 +chr1 4754241 4754864 MACS_peak_129 329.74 +chr1 4755088 4755200 MACS_peak_130 100.24 +chr1 4755722 4756029 MACS_peak_131 205.50 +chr1 4756768 4756880 MACS_peak_132 100.24 +chr1 4757199 4758615 MACS_peak_133 569.34 +chr1 4758753 4762214 MACS_peak_134 3100.00 +chr1 4763207 4763319 MACS_peak_135 100.24 +chr1 4763614 4763726 MACS_peak_136 100.24 +chr1 4763998 4764322 MACS_peak_137 358.13 +chr1 4764568 4764850 MACS_peak_138 133.23 +chr1 4765104 4765765 MACS_peak_139 291.01 +chr1 4765892 4766067 MACS_peak_140 100.24 +chr1 4766232 4766420 MACS_peak_141 100.24 +chr1 4766539 4767148 MACS_peak_142 367.65 +chr1 4767417 4767529 MACS_peak_143 100.24 +chr1 4768245 4768357 MACS_peak_144 100.24 +chr1 4768587 4768870 MACS_peak_145 170.00 +chr1 4768989 4769272 MACS_peak_146 133.17 +chr1 4769463 4769684 MACS_peak_147 174.88 +chr1 4769861 4770236 MACS_peak_148 200.29 +chr1 4770689 4771270 MACS_peak_149 224.05 +chr1 4771393 4772502 MACS_peak_150 1799.39 +chr1 4772633 4772916 MACS_peak_151 133.17 +chr1 4773121 4773284 MACS_peak_152 100.24 +chr1 4773476 4773614 MACS_peak_153 137.07 +chr1 4773827 4774279 MACS_peak_154 159.83 +chr1 4774510 4774622 MACS_peak_155 100.24 +chr1 4775041 4775694 MACS_peak_156 291.49 +chr1 4775832 4775944 MACS_peak_157 100.24 +chr1 4776166 4776310 MACS_peak_158 137.07 +chr1 4776506 4776851 MACS_peak_159 165.70 +chr1 4777100 4777321 MACS_peak_160 137.07 +chr1 4777505 4777617 MACS_peak_161 100.24 +chr1 4777764 4778298 MACS_peak_162 156.21 +chr1 4778680 4778792 MACS_peak_163 100.24 +chr1 4779265 4779377 MACS_peak_164 100.24 +chr1 4780814 4780926 MACS_peak_165 100.24 +chr1 4781238 4781436 MACS_peak_166 137.07 +chr1 4781600 4781712 MACS_peak_167 100.24 +chr1 4784249 4784487 MACS_peak_168 173.76 +chr1 4784800 4784912 MACS_peak_169 100.24 +chr1 4785500 4785612 MACS_peak_170 100.24 +chr1 4786820 4787357 MACS_peak_171 226.44 +chr1 4787570 4787682 MACS_peak_172 100.24 +chr1 4789440 4789978 MACS_peak_173 262.47 +chr1 4790257 4790424 MACS_peak_174 100.24 +chr1 4790723 4791308 MACS_peak_175 223.84 +chr1 4791871 4792641 MACS_peak_176 392.73 +chr1 4792756 4793323 MACS_peak_177 189.52 +chr1 4794493 4794929 MACS_peak_178 232.77 +chr1 4795046 4795357 MACS_peak_179 131.53 +chr1 4795495 4795607 MACS_peak_180 100.24 +chr1 4796218 4796432 MACS_peak_181 174.88 +chr1 4796841 4796953 MACS_peak_182 100.24 +chr1 4797267 4797499 MACS_peak_183 99.89 +chr1 4797910 4798022 MACS_peak_184 100.24 +chr1 4799151 4799263 MACS_peak_185 100.24 +chr1 4799518 4800266 MACS_peak_186 216.37 +chr1 4800415 4800527 MACS_peak_187 100.24 +chr1 4800989 4801101 MACS_peak_188 100.24 +chr1 4801344 4802288 MACS_peak_189 311.70 +chr1 4802600 4802712 MACS_peak_190 100.24 +chr1 4802944 4803056 MACS_peak_191 100.24 +chr1 4803408 4803520 MACS_peak_192 100.24 +chr1 4803899 4804011 MACS_peak_193 100.24 +chr1 4804278 4804390 MACS_peak_194 100.24 +chr1 4804716 4805427 MACS_peak_195 360.26 +chr1 4805843 4806018 MACS_peak_196 100.24 +chr1 4806294 4806406 MACS_peak_197 100.24 +chr1 4806523 4806849 MACS_peak_198 241.61 +chr1 4807024 4807205 MACS_peak_199 174.88 +chr1 4807520 4807740 MACS_peak_200 100.24 +chr1 4808021 4808133 MACS_peak_201 100.24 +chr1 4809641 4810406 MACS_peak_202 320.82 +chr1 4810853 4812088 MACS_peak_203 508.29 +chr1 4812253 4812665 MACS_peak_204 234.49 +chr1 4813090 4813202 MACS_peak_205 100.24 +chr1 4813466 4813836 MACS_peak_206 200.64 +chr1 4814068 4814180 MACS_peak_207 100.24 +chr1 4814343 4814700 MACS_peak_208 129.13 +chr1 4814902 4815014 MACS_peak_209 100.24 +chr1 4815190 4815343 MACS_peak_210 174.88 +chr1 4815570 4816098 MACS_peak_211 191.37 +chr1 4816683 4817303 MACS_peak_212 222.07 +chr1 4817449 4817735 MACS_peak_213 97.17 +chr1 4818299 4818411 MACS_peak_214 100.24 +chr1 4819699 4819870 MACS_peak_215 137.07 +chr1 4820406 4821178 MACS_peak_216 429.22 +chr1 4821318 4821821 MACS_peak_217 192.64 +chr1 4822130 4822242 MACS_peak_218 100.24 +chr1 4822509 4823010 MACS_peak_219 192.74 +chr1 4823526 4823638 MACS_peak_220 100.24 +chr1 4823838 4823996 MACS_peak_221 174.88 +chr1 4824146 4824258 MACS_peak_222 100.24 +chr1 4824694 4824806 MACS_peak_223 100.24 +chr1 4825207 4825319 MACS_peak_224 100.24 +chr1 4825494 4825606 MACS_peak_225 100.24 +chr1 4825793 4825905 MACS_peak_226 100.24 +chr1 4827008 4827120 MACS_peak_227 100.24 +chr1 4827550 4827866 MACS_peak_228 95.87 +chr1 4828619 4829306 MACS_peak_229 184.51 +chr1 4829921 4830483 MACS_peak_230 409.14 +chr1 4830656 4830878 MACS_peak_231 137.07 +chr1 4831394 4831506 MACS_peak_232 100.24 +chr1 4831844 4831956 MACS_peak_233 100.24 +chr1 4832109 4832299 MACS_peak_234 137.07 +chr1 4832653 4832765 MACS_peak_235 100.24 +chr1 4833194 4833306 MACS_peak_236 100.24 +chr1 4833562 4834290 MACS_peak_237 322.98 +chr1 4834418 4834761 MACS_peak_238 129.83 +chr1 4835007 4835561 MACS_peak_239 225.49 +chr1 4835772 4835884 MACS_peak_240 100.24 +chr1 4836111 4836342 MACS_peak_241 136.69 +chr1 4836700 4836872 MACS_peak_242 100.24 +chr1 4837011 4837326 MACS_peak_243 95.91 +chr1 4837787 4838061 MACS_peak_244 97.73 +chr1 4838509 4838621 MACS_peak_245 100.24 +chr1 4838750 4839072 MACS_peak_246 130.92 +chr1 4839375 4839615 MACS_peak_247 211.91 +chr1 4840334 4840446 MACS_peak_248 100.24 +chr1 4841036 4841160 MACS_peak_249 137.07 +chr1 4841416 4841762 MACS_peak_250 165.63 +chr1 4842486 4842598 MACS_peak_251 100.24 +chr1 4842727 4843432 MACS_peak_252 183.84 +chr1 4843856 4844363 MACS_peak_253 301.38 +chr1 4844645 4845031 MACS_peak_254 163.26 +chr1 4845512 4845972 MACS_peak_255 159.45 +chr1 4846211 4846346 MACS_peak_256 213.48 +chr1 4846821 4847168 MACS_peak_257 129.63 +chr1 4847291 4847699 MACS_peak_258 126.81 +chr1 4847873 4848128 MACS_peak_259 98.66 +chr1 4848823 4848969 MACS_peak_260 137.07 +chr1 4849335 4850291 MACS_peak_261 453.17 +chr1 4850534 4850878 MACS_peak_262 129.78 +chr1 4851485 4851770 MACS_peak_263 97.21 +chr1 4852224 4852336 MACS_peak_264 100.24 +chr1 4852629 4852893 MACS_peak_265 171.51 +chr1 4853247 4853359 MACS_peak_266 100.24 +chr1 4853500 4853612 MACS_peak_267 100.24 +chr1 4854342 4854454 MACS_peak_268 100.24 +chr1 4854696 4854915 MACS_peak_269 137.07 +chr1 4855160 4855749 MACS_peak_270 154.08 +chr1 4856482 4857364 MACS_peak_271 211.36 +chr1 4857573 4857697 MACS_peak_272 213.48 +chr1 4857830 4857942 MACS_peak_273 100.24 +chr1 4858204 4858599 MACS_peak_274 235.78 +chr1 4858812 4859245 MACS_peak_275 125.78 +chr1 4859843 4859955 MACS_peak_276 100.24 +chr1 4860077 4860209 MACS_peak_277 137.07 +chr1 4860573 4861449 MACS_peak_278 458.48 +chr1 4861747 4861976 MACS_peak_279 100.06 +chr1 4862268 4862651 MACS_peak_280 93.36 +chr1 4863414 4863526 MACS_peak_281 100.24 +chr1 4864845 4865021 MACS_peak_282 100.24 +chr1 4865297 4865766 MACS_peak_283 230.56 +chr1 4865923 4866035 MACS_peak_284 100.24 +chr1 4866382 4866494 MACS_peak_285 100.24 +chr1 4867682 4867807 MACS_peak_286 137.07 +chr1 4868654 4868766 MACS_peak_287 100.24 +chr1 4868930 4869268 MACS_peak_288 94.99 +chr1 4869676 4869788 MACS_peak_289 100.24 +chr1 4872133 4872544 MACS_peak_290 271.82 +chr1 4872662 4873337 MACS_peak_291 254.59 +chr1 4874062 4874473 MACS_peak_292 271.82 +chr1 4874975 4875211 MACS_peak_293 173.94 +chr1 4876698 4876810 MACS_peak_294 100.24 +chr1 4877028 4877284 MACS_peak_295 98.61 +chr1 4877427 4877588 MACS_peak_296 100.24 +chr1 4878177 4878289 MACS_peak_297 100.24 +chr1 4878676 4878788 MACS_peak_298 100.24 +chr1 4879245 4880188 MACS_peak_299 209.33 +chr1 4880427 4881235 MACS_peak_300 318.45 +chr1 4881879 4882060 MACS_peak_301 137.07 +chr1 4882471 4883064 MACS_peak_302 295.25 +chr1 4883301 4883864 MACS_peak_303 155.06 +chr1 4884407 4884593 MACS_peak_304 100.24 +chr1 4884796 4884908 MACS_peak_305 100.24 +chr1 4885346 4886192 MACS_peak_306 212.63 +chr1 4886722 4886834 MACS_peak_307 100.24 +chr1 4887003 4887328 MACS_peak_308 130.76 +chr1 4887618 4887730 MACS_peak_309 100.24 +chr1 4889449 4889763 MACS_peak_310 95.95 +chr1 4890020 4890132 MACS_peak_311 100.24 +chr1 4890331 4890463 MACS_peak_312 137.07 +chr1 4890662 4891095 MACS_peak_313 270.01 +chr1 4891457 4893061 MACS_peak_314 701.27 +chr1 4893216 4893887 MACS_peak_315 290.43 +chr1 4894234 4894346 MACS_peak_316 100.24 +chr1 4894464 4894730 MACS_peak_317 171.34 +chr1 4895365 4895858 MACS_peak_318 157.95 +chr1 4896603 4896715 MACS_peak_319 100.24 +chr1 4897044 4897793 MACS_peak_320 216.33 +chr1 4898184 4898296 MACS_peak_321 100.24 +chr1 4898589 4898701 MACS_peak_322 100.24 +chr1 4898838 4899317 MACS_peak_323 124.03 +chr1 4899461 4900031 MACS_peak_324 296.80 +chr1 4900244 4900356 MACS_peak_325 100.24 +chr1 4900490 4900638 MACS_peak_326 137.07 +chr1 4900927 4901039 MACS_peak_327 100.24 +chr1 4901371 4901558 MACS_peak_328 137.07 +chr1 4901767 4902496 MACS_peak_329 359.06 +chr1 4902621 4903202 MACS_peak_330 259.79 +chr1 4903396 4903692 MACS_peak_331 169.02 +chr1 4903871 4903983 MACS_peak_332 100.24 +chr1 4904596 4904708 MACS_peak_333 100.24 +chr1 4905302 4905414 MACS_peak_334 100.24 +chr1 4905612 4906211 MACS_peak_335 294.86 +chr1 4906407 4906662 MACS_peak_336 172.26 +chr1 4907188 4907339 MACS_peak_337 100.24 +chr1 4908299 4909216 MACS_peak_338 455.70 +chr1 4909542 4909654 MACS_peak_339 100.24 +chr1 4909952 4910103 MACS_peak_340 100.24 +chr1 4910247 4910755 MACS_peak_341 192.38 +chr1 4910931 4911043 MACS_peak_342 100.24 +chr1 4912153 4912290 MACS_peak_343 137.07 +chr1 4913430 4913601 MACS_peak_344 100.24 +chr1 4913916 4914526 MACS_peak_345 153.32 +chr1 4914785 4915085 MACS_peak_346 132.15 +chr1 4915254 4916101 MACS_peak_347 351.90 +chr1 4916248 4916612 MACS_peak_348 128.80 +chr1 4916731 4916898 MACS_peak_349 100.24 +chr1 4917041 4918520 MACS_peak_350 565.94 +chr1 4918971 4919511 MACS_peak_351 155.97 +chr1 4920143 4920281 MACS_peak_352 137.07 +chr1 4920830 4920976 MACS_peak_353 174.88 +chr1 4921156 4921616 MACS_peak_354 231.14 +chr1 4921783 4922072 MACS_peak_355 132.80 +chr1 4922200 4922312 MACS_peak_356 100.24 +chr1 4922698 4922810 MACS_peak_357 100.24 +chr1 4922952 4923064 MACS_peak_358 100.24 +chr1 4923711 4923825 MACS_peak_359 137.07 +chr1 4924847 4925134 MACS_peak_360 169.69 +chr1 4925374 4925521 MACS_peak_361 137.07 +chr1 4926127 4926628 MACS_peak_362 228.55 +chr1 4926755 4927616 MACS_peak_363 351.11 +chr1 4927845 4928143 MACS_peak_364 168.88 +chr1 4928391 4929764 MACS_peak_365 431.16 +chr1 4929891 4930203 MACS_peak_366 131.47 +chr1 4930358 4930563 MACS_peak_367 100.24 +chr1 4930982 4931172 MACS_peak_368 100.24 +chr1 4931361 4931660 MACS_peak_369 168.80 +chr1 4932382 4932963 MACS_peak_370 224.05 +chr1 4933440 4933552 MACS_peak_371 100.24 +chr1 4933681 4934002 MACS_peak_372 204.34 +chr1 4934226 4934700 MACS_peak_373 266.86 +chr1 4934820 4935023 MACS_peak_374 100.24 +chr1 4935896 4936217 MACS_peak_375 280.40 +chr1 4936341 4937067 MACS_peak_376 217.28 +chr1 4937317 4937429 MACS_peak_377 100.24 +chr1 4937921 4938033 MACS_peak_378 100.24 +chr1 4944882 4945123 MACS_peak_379 290.36 +chr1 4945522 4945861 MACS_peak_380 130.03 +chr1 4946020 4946166 MACS_peak_381 137.07 +chr1 4946436 4946584 MACS_peak_382 137.07 +chr1 4946710 4946822 MACS_peak_383 100.24 +chr1 4946951 4947336 MACS_peak_384 163.31 +chr1 4948023 4948135 MACS_peak_385 100.24 +chr1 4948535 4948658 MACS_peak_386 137.07 +chr1 4951023 4951135 MACS_peak_387 100.24 +chr1 4952397 4953059 MACS_peak_388 185.48 +chr1 4953377 4953609 MACS_peak_389 136.62 +chr1 4953840 4954681 MACS_peak_390 246.95 +chr1 4955012 4956131 MACS_peak_391 443.60 +chr1 4956418 4956838 MACS_peak_392 161.43 +chr1 4957163 4957694 MACS_peak_393 299.57 +chr1 4958356 4958529 MACS_peak_394 100.24 +chr1 4958823 4959148 MACS_peak_395 166.99 +chr1 4959772 4960322 MACS_peak_396 298.20 +chr1 4960576 4962064 MACS_peak_397 636.53 +chr1 4962737 4963409 MACS_peak_398 326.45 +chr1 4963700 4963974 MACS_peak_399 133.73 +chr1 4965851 4966062 MACS_peak_400 100.24 +chr1 4966437 4967281 MACS_peak_401 352.07 +chr1 4967476 4967641 MACS_peak_402 100.24 +chr1 4967813 4968456 MACS_peak_403 220.97 +chr1 4968607 4968752 MACS_peak_404 174.88 +chr1 4968965 4969286 MACS_peak_405 95.66 +chr1 4969410 4969822 MACS_peak_406 126.64 +chr1 4970372 4970484 MACS_peak_407 100.24 +chr1 4975200 4975343 MACS_peak_408 174.88 +chr1 4975521 4975633 MACS_peak_409 100.24 +chr1 4975762 4975980 MACS_peak_410 100.24 +chr1 4976829 4976941 MACS_peak_411 100.24 +chr1 4978309 4978421 MACS_peak_412 100.24 +chr1 4979774 4980223 MACS_peak_413 195.59 +chr1 4980423 4980535 MACS_peak_414 100.24 +chr1 4980817 4980991 MACS_peak_415 100.24 +chr1 4981234 4981537 MACS_peak_416 168.51 +chr1 4981655 4982010 MACS_peak_417 165.08 +chr1 4982893 4983037 MACS_peak_418 137.07 +chr1 4984463 4984708 MACS_peak_419 135.67 +chr1 4985269 4985381 MACS_peak_420 100.24 +chr1 4986003 4986204 MACS_peak_421 100.24 +chr1 4987600 4987712 MACS_peak_422 100.24 +chr1 4988896 4989008 MACS_peak_423 100.24 +chr1 4990354 4990466 MACS_peak_424 100.24 +chr1 4991245 4991357 MACS_peak_425 100.24 +chr1 4992001 4992258 MACS_peak_426 98.56 +chr1 4992834 4993305 MACS_peak_427 194.35 +chr1 4993542 4993654 MACS_peak_428 100.24 +chr1 4993878 4994124 MACS_peak_429 135.60 +chr1 4994717 4995335 MACS_peak_430 187.27 +chr1 4995469 4996377 MACS_peak_431 492.84 +chr1 4996497 4996609 MACS_peak_432 100.24 +chr1 4996828 4997058 MACS_peak_433 100.01 +chr1 4997280 4997406 MACS_peak_434 137.07 +chr1 4997521 4997646 MACS_peak_435 137.07 +chr1 4997838 4998328 MACS_peak_436 193.32 +chr1 4998584 4998978 MACS_peak_437 273.29 +chr1 4999395 4999507 MACS_peak_438 100.24 +chr1 5000025 5000145 MACS_peak_439 137.07 +chr1 5000445 5000681 MACS_peak_440 99.67 +chr1 5002097 5002492 MACS_peak_441 162.76 +chr1 5003083 5003284 MACS_peak_442 100.24 +chr1 5003661 5004017 MACS_peak_443 165.01 +chr1 5004225 5004846 MACS_peak_444 293.45 +chr1 5004962 5005074 MACS_peak_445 100.24 +chr1 5005414 5005526 MACS_peak_446 100.24 +chr1 5005899 5006531 MACS_peak_447 221.49 +chr1 5006687 5006799 MACS_peak_448 100.24 +chr1 5007121 5007233 MACS_peak_449 100.24 +chr1 5007621 5007888 MACS_peak_450 98.06 +chr1 5008386 5008804 MACS_peak_451 161.53 +chr1 5009297 5009455 MACS_peak_452 100.24 +chr1 5009800 5009919 MACS_peak_453 137.07 +chr1 5010164 5010383 MACS_peak_454 100.24 +chr1 5010702 5010814 MACS_peak_455 100.24 +chr1 5011318 5011430 MACS_peak_456 100.24 +chr1 5011570 5011904 MACS_peak_457 130.29 +chr1 5012040 5012172 MACS_peak_458 213.48 +chr1 5012312 5012452 MACS_peak_459 174.88 +chr1 5013118 5013359 MACS_peak_460 99.40 +chr1 5013518 5013658 MACS_peak_461 174.88 +chr1 5013881 5013993 MACS_peak_462 100.24 +chr1 5014248 5014742 MACS_peak_463 228.98 +chr1 5015114 5015226 MACS_peak_464 100.24 +chr1 5015801 5016141 MACS_peak_465 129.98 +chr1 5016467 5016756 MACS_peak_466 132.80 +chr1 5016937 5017049 MACS_peak_467 100.24 +chr1 5017244 5017888 MACS_peak_468 256.22 +chr1 5018361 5018825 MACS_peak_469 230.88 +chr1 5018988 5019283 MACS_peak_470 132.45 +chr1 5019483 5019735 MACS_peak_471 135.18 +chr1 5019878 5020096 MACS_peak_472 100.24 +chr1 5020521 5020633 MACS_peak_473 100.24 +chr1 5021108 5021423 MACS_peak_474 95.91 +chr1 5021637 5021749 MACS_peak_475 100.24 +chr1 5021983 5022543 MACS_peak_476 189.84 +chr1 5022857 5023545 MACS_peak_477 218.91 +chr1 5023746 5023858 MACS_peak_478 100.24 +chr1 5023989 5024146 MACS_peak_479 100.24 +chr1 5024463 5024752 MACS_peak_480 245.27 +chr1 5024980 5025092 MACS_peak_481 100.24 +chr1 5025520 5025734 MACS_peak_482 137.07 +chr1 5032611 5032723 MACS_peak_483 100.24 +chr1 5033023 5033254 MACS_peak_484 99.95 +chr1 5033681 5033793 MACS_peak_485 100.24 +chr1 5034513 5034625 MACS_peak_486 100.24 +chr1 5035054 5035185 MACS_peak_487 137.07 +chr1 5038790 5039022 MACS_peak_488 136.62 +chr1 5039491 5039790 MACS_peak_489 96.59 +chr1 5040037 5040149 MACS_peak_490 100.24 +chr1 5042044 5042156 MACS_peak_491 100.24 +chr1 5044343 5044455 MACS_peak_492 100.24 +chr1 5045148 5045303 MACS_peak_493 100.24 +chr1 5045444 5045580 MACS_peak_494 137.07 +chr1 5045759 5046137 MACS_peak_495 274.73 +chr1 5046459 5046932 MACS_peak_496 124.25 +chr1 5047196 5047790 MACS_peak_497 188.30 +chr1 5048329 5048441 MACS_peak_498 100.24 +chr1 5051379 5051491 MACS_peak_499 100.24 +chr1 5054182 5054620 MACS_peak_500 160.51 +chr1 5054821 5054933 MACS_peak_501 100.24 +chr1 5055158 5055270 MACS_peak_502 100.24 +chr1 5055388 5055791 MACS_peak_503 272.50 +chr1 5056110 5056222 MACS_peak_504 100.24 +chr1 5056524 5056951 MACS_peak_505 161.07 +chr1 5057086 5057694 MACS_peak_506 222.67 +chr1 5058767 5058879 MACS_peak_507 100.24 +chr1 5059021 5059659 MACS_peak_508 256.54 +chr1 5060172 5060284 MACS_peak_509 100.24 +chr1 5060462 5060574 MACS_peak_510 100.24 +chr1 5061165 5061359 MACS_peak_511 137.07 +chr1 5061551 5062254 MACS_peak_512 585.63 +chr1 5062414 5062526 MACS_peak_513 100.24 +chr1 5062713 5062989 MACS_peak_514 133.60 +chr1 5063187 5063299 MACS_peak_515 100.24 +chr1 5064348 5064562 MACS_peak_516 174.88 +chr1 5064956 5065068 MACS_peak_517 100.24 +chr1 5065226 5065447 MACS_peak_518 174.88 +chr1 5065611 5066438 MACS_peak_519 213.32 +chr1 5066845 5066957 MACS_peak_520 100.24 +chr1 5067268 5067380 MACS_peak_521 100.24 +chr1 5067511 5067627 MACS_peak_522 137.07 +chr1 5074120 5074316 MACS_peak_523 174.88 +chr1 5074836 5074948 MACS_peak_524 100.24 +chr1 5075666 5076224 MACS_peak_525 225.27 +chr1 5076921 5077525 MACS_peak_526 258.45 +chr1 5077697 5079141 MACS_peak_527 428.10 +chr1 5079395 5079507 MACS_peak_528 100.24 +chr1 5079650 5079862 MACS_peak_529 100.24 +chr1 5081683 5081832 MACS_peak_530 137.07 +chr1 5081976 5082088 MACS_peak_531 100.24 +chr1 5082876 5083204 MACS_peak_532 95.38 +chr1 5083349 5083507 MACS_peak_533 100.24 +chr1 5083630 5083769 MACS_peak_534 137.07 +chr1 5084103 5084215 MACS_peak_535 100.24 +chr1 5084548 5084886 MACS_peak_536 130.08 +chr1 5085651 5085824 MACS_peak_537 137.07 +chr1 5086191 5086343 MACS_peak_538 100.24 +chr1 5086595 5087134 MACS_peak_539 190.83 +chr1 5087415 5087527 MACS_peak_540 100.24 +chr1 5087866 5088086 MACS_peak_541 137.07 +chr1 5088244 5088578 MACS_peak_542 203.30 +chr1 5089007 5089195 MACS_peak_543 137.07 +chr1 5089715 5089831 MACS_peak_544 137.07 +chr1 5090015 5090353 MACS_peak_545 130.08 +chr1 5090497 5090609 MACS_peak_546 100.24 +chr1 5091306 5091577 MACS_peak_547 133.92 +chr1 5091972 5092130 MACS_peak_548 100.24 +chr1 5092602 5092857 MACS_peak_549 172.26 +chr1 5093070 5093254 MACS_peak_550 100.24 +chr1 5093580 5094069 MACS_peak_551 158.12 +chr1 5094211 5094776 MACS_peak_552 485.14 +chr1 5094935 5095339 MACS_peak_553 272.42 +chr1 5095631 5095955 MACS_peak_554 130.82 +chr1 5096075 5096386 MACS_peak_555 131.53 +chr1 5097061 5097359 MACS_peak_556 96.63 +chr1 5097863 5098163 MACS_peak_557 206.10 +chr1 5098989 5099101 MACS_peak_558 100.24 +chr1 5099702 5099814 MACS_peak_559 100.24 +chr1 5100443 5100725 MACS_peak_560 97.35 +chr1 5105969 5106193 MACS_peak_561 174.88 +chr1 5106329 5106441 MACS_peak_562 100.24 +chr1 5106565 5106677 MACS_peak_563 100.24 +chr1 5106814 5107170 MACS_peak_564 238.93 +chr1 5107427 5107660 MACS_peak_565 136.54 +chr1 5107833 5108160 MACS_peak_566 95.42 +chr1 5108453 5108565 MACS_peak_567 100.24 +chr1 5108705 5108860 MACS_peak_568 100.24 +chr1 5109105 5109217 MACS_peak_569 100.24 +chr1 5109576 5109688 MACS_peak_570 100.24 +chr1 5110000 5110112 MACS_peak_571 100.24 +chr1 5110475 5111286 MACS_peak_572 213.91 +chr1 5111879 5112070 MACS_peak_573 100.24 +chr1 5112186 5112435 MACS_peak_574 135.39 +chr1 5112580 5112692 MACS_peak_575 100.24 +chr1 5113545 5113657 MACS_peak_576 100.24 +chr1 5114104 5114508 MACS_peak_577 310.25 +chr1 5115038 5115191 MACS_peak_578 100.24 +chr1 5115640 5115752 MACS_peak_579 100.24 +chr1 5116113 5116531 MACS_peak_580 161.53 +chr1 5116969 5117081 MACS_peak_581 100.24 +chr1 5118784 5118914 MACS_peak_582 213.48 +chr1 5119112 5119565 MACS_peak_583 125.00 +chr1 5119931 5120133 MACS_peak_584 100.24 +chr1 5120509 5120783 MACS_peak_585 97.73 +chr1 5122513 5123111 MACS_peak_586 331.52 +chr1 5124258 5124546 MACS_peak_587 132.86 +chr1 5125243 5125355 MACS_peak_588 100.24 +chr1 5125474 5126301 MACS_peak_589 247.53 +chr1 5126879 5127188 MACS_peak_590 96.16 +chr1 5127510 5127622 MACS_peak_591 100.24 +chr1 5128418 5128797 MACS_peak_592 200.01 +chr1 5129100 5129423 MACS_peak_593 130.87 +chr1 5129639 5130227 MACS_peak_594 295.59 +chr1 5130392 5130670 MACS_peak_595 208.08 +chr1 5131190 5131730 MACS_peak_596 226.27 +chr1 5131882 5132669 MACS_peak_597 428.13 +chr1 5133036 5133148 MACS_peak_598 100.24 +chr1 5133406 5133811 MACS_peak_599 162.22 +chr1 5134265 5134418 MACS_peak_600 100.24 +chr1 5134545 5135189 MACS_peak_601 220.92 +chr1 5135648 5135760 MACS_peak_602 100.24 +chr1 5135922 5136197 MACS_peak_603 133.66 +chr1 5137176 5137712 MACS_peak_604 190.98 +chr1 5138380 5138492 MACS_peak_605 100.24 +chr1 5138673 5138785 MACS_peak_606 100.24 +chr1 5139178 5139447 MACS_peak_607 171.10 +chr1 5140390 5140502 MACS_peak_608 100.24 +chr1 5141274 5141386 MACS_peak_609 100.24 +chr1 5141930 5142225 MACS_peak_610 96.76 +chr1 5142569 5143225 MACS_peak_611 220.36 +chr1 5143538 5143758 MACS_peak_612 137.07 +chr1 5144459 5144571 MACS_peak_613 100.24 +chr1 5145367 5145546 MACS_peak_614 137.07 +chr1 5146746 5146858 MACS_peak_615 100.24 +chr1 5147216 5147328 MACS_peak_616 100.24 +chr1 5148439 5148925 MACS_peak_617 193.53 +chr1 5149170 5149620 MACS_peak_618 195.54 +chr1 5149975 5150169 MACS_peak_619 137.07 +chr1 5150944 5151056 MACS_peak_620 100.24 +chr1 5151214 5151612 MACS_peak_621 235.55 +chr1 5151849 5152235 MACS_peak_622 163.26 +chr1 5152352 5152662 MACS_peak_623 131.58 +chr1 5152894 5153006 MACS_peak_624 100.24 +chr1 5153179 5153550 MACS_peak_625 128.46 +chr1 5153683 5154461 MACS_peak_626 249.65 +chr1 5154978 5155690 MACS_peak_627 217.87 +chr1 5156139 5156251 MACS_peak_628 100.24 +chr1 5157081 5157193 MACS_peak_629 100.24 +chr1 5159033 5159145 MACS_peak_630 100.24 +chr1 5159942 5160260 MACS_peak_631 95.79 +chr1 5160427 5160539 MACS_peak_632 100.24 +chr1 5161207 5161319 MACS_peak_633 100.24 +chr1 5161624 5161843 MACS_peak_634 100.24 +chr1 5162094 5162256 MACS_peak_635 100.24 +chr1 5162373 5162485 MACS_peak_636 100.24 +chr1 5164184 5164730 MACS_peak_637 225.94 +chr1 5165964 5166076 MACS_peak_638 100.24 +chr1 5166208 5166320 MACS_peak_639 100.24 +chr1 5166857 5167382 MACS_peak_640 227.13 +chr1 5167811 5167961 MACS_peak_641 252.75 +chr1 5168164 5168628 MACS_peak_642 230.88 +chr1 5168852 5168964 MACS_peak_643 100.24 +chr1 5169149 5169385 MACS_peak_644 136.32 +chr1 5170312 5170424 MACS_peak_645 100.24 +chr1 5170892 5171004 MACS_peak_646 100.24 +chr1 5171504 5171624 MACS_peak_647 137.07 +chr1 5172575 5172847 MACS_peak_648 97.82 +chr1 5173299 5173617 MACS_peak_649 131.14 +chr1 5174320 5175248 MACS_peak_650 677.53 +chr1 5176172 5176514 MACS_peak_651 202.69 +chr1 5176705 5177327 MACS_peak_652 403.86 +chr1 5177495 5178136 MACS_peak_653 292.21 +chr1 5178335 5178447 MACS_peak_654 100.24 +chr1 5178577 5179078 MACS_peak_655 264.94 +chr1 5179327 5179439 MACS_peak_656 100.24 +chr1 5179573 5179930 MACS_peak_657 201.57 +chr1 5180202 5180486 MACS_peak_658 133.11 +chr1 5187026 5187438 MACS_peak_659 126.64 +chr1 5189520 5189632 MACS_peak_660 100.24 +chr1 5190641 5190753 MACS_peak_661 100.24 +chr1 5193903 5194083 MACS_peak_662 137.07 +chr1 5194313 5194507 MACS_peak_663 100.24 +chr1 5194886 5195134 MACS_peak_664 211.06 +chr1 5195426 5195539 MACS_peak_665 174.88 +chr1 5195775 5195951 MACS_peak_666 137.07 +chr1 5196298 5197058 MACS_peak_667 215.89 +chr1 5197469 5197637 MACS_peak_668 100.24 +chr1 5197796 5198864 MACS_peak_669 591.38 +chr1 5199145 5199310 MACS_peak_670 174.88 +chr1 5199643 5199824 MACS_peak_671 137.07 +chr1 5200158 5200523 MACS_peak_672 93.99 +chr1 5200710 5201367 MACS_peak_673 185.68 +chr1 5201497 5202378 MACS_peak_674 531.75 +chr1 5202917 5203141 MACS_peak_675 213.48 +chr1 5203327 5203439 MACS_peak_676 100.24 +chr1 5204084 5204196 MACS_peak_677 100.24 +chr1 5204570 5204682 MACS_peak_678 100.24 +chr1 5205197 5205309 MACS_peak_679 100.24 +chr1 5205592 5205787 MACS_peak_680 137.07 +chr1 5205929 5206041 MACS_peak_681 100.24 +chr1 5206900 5207012 MACS_peak_682 100.24 +chr1 5207183 5207396 MACS_peak_683 137.07 +chr1 5207524 5207736 MACS_peak_684 137.07 +chr1 5207873 5209950 MACS_peak_685 746.37 +chr1 5210089 5210201 MACS_peak_686 100.24 +chr1 5210451 5210563 MACS_peak_687 100.24 +chr1 5211018 5211130 MACS_peak_688 100.24 +chr1 5211276 5211388 MACS_peak_689 100.24 +chr1 5211564 5211734 MACS_peak_690 100.24 +chr1 5212067 5212435 MACS_peak_691 275.66 +chr1 5212594 5212753 MACS_peak_692 100.24 +chr1 5212901 5213013 MACS_peak_693 100.24 +chr1 5213338 5213697 MACS_peak_694 201.42 +chr1 5214024 5214232 MACS_peak_695 137.07 +chr1 5214383 5214747 MACS_peak_696 128.80 +chr1 5214900 5215012 MACS_peak_697 100.24 +chr1 5215554 5215666 MACS_peak_698 100.24 +chr1 5216098 5216421 MACS_peak_699 95.58 +chr1 5216849 5217112 MACS_peak_700 171.59 +chr1 5217261 5217531 MACS_peak_701 208.84 +chr1 5217649 5217761 MACS_peak_702 100.24 +chr1 5218122 5218337 MACS_peak_703 137.07 +chr1 5218836 5219185 MACS_peak_704 165.45 +chr1 5219969 5220835 MACS_peak_705 350.84 +chr1 5220968 5221934 MACS_peak_706 416.57 +chr1 5222619 5223011 MACS_peak_707 127.51 +chr1 5223269 5223882 MACS_peak_708 257.93 +chr1 5224180 5225221 MACS_peak_709 483.94 +chr1 5225717 5226312 MACS_peak_710 223.32 +chr1 5226601 5226880 MACS_peak_711 97.49 +chr1 5227642 5227754 MACS_peak_712 100.24 +chr1 5229513 5229625 MACS_peak_713 100.24 +chr1 5229772 5230341 MACS_peak_714 260.52 +chr1 5230857 5231047 MACS_peak_715 137.07 +chr1 5231309 5231610 MACS_peak_716 96.50 +chr1 5232430 5232542 MACS_peak_717 100.24 +chr1 5232868 5233105 MACS_peak_718 136.25 +chr1 5234222 5234548 MACS_peak_719 130.71 +chr1 5234732 5234930 MACS_peak_720 137.07 +chr1 5235612 5236082 MACS_peak_721 158.98 +chr1 5236311 5236423 MACS_peak_722 100.24 +chr1 5236609 5236721 MACS_peak_723 100.24 +chr1 5237018 5237130 MACS_peak_724 100.24 +chr1 5237454 5237566 MACS_peak_725 100.24 +chr1 5238037 5238329 MACS_peak_726 132.62 +chr1 5239958 5240439 MACS_peak_727 229.79 +chr1 5240929 5241239 MACS_peak_728 168.02 +chr1 5247940 5248227 MACS_peak_729 132.92 +chr1 5248801 5249638 MACS_peak_730 179.37 +chr1 5249894 5250597 MACS_peak_731 434.51 +chr1 5250980 5251895 MACS_peak_732 278.31 +chr1 5253201 5253499 MACS_peak_733 206.27 +chr1 5253899 5254138 MACS_peak_734 136.10 +chr1 5254545 5254925 MACS_peak_735 199.94 +chr1 5255688 5255800 MACS_peak_736 100.24 +chr1 5256047 5256432 MACS_peak_737 199.60 +chr1 5256609 5256721 MACS_peak_738 100.24 +chr1 5257206 5257318 MACS_peak_739 100.24 +chr1 5257448 5257698 MACS_peak_740 135.32 +chr1 5257987 5258099 MACS_peak_741 100.24 +chr1 5264494 5264931 MACS_peak_742 160.56 +chr1 5265092 5265455 MACS_peak_743 164.59 +chr1 5266250 5266425 MACS_peak_744 100.24 +chr1 5267306 5268160 MACS_peak_745 351.50 +chr1 5269815 5269927 MACS_peak_746 100.24 +chr1 5270319 5270873 MACS_peak_747 372.17 +chr1 5271490 5271846 MACS_peak_748 129.18 +chr1 5272438 5272660 MACS_peak_749 100.24 +chr1 5272916 5273028 MACS_peak_750 100.24 +chr1 5273367 5273479 MACS_peak_751 100.24 +chr1 5273651 5273916 MACS_peak_752 171.42 +chr1 5274301 5274503 MACS_peak_753 100.24 +chr1 5274805 5274917 MACS_peak_754 100.24 +chr1 5275154 5275487 MACS_peak_755 166.46 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5292542 MACS_peak_779 194.29 +chr1 5292725 5293056 MACS_peak_780 166.60 +chr1 5293630 5293742 MACS_peak_781 100.24 +chr1 5294389 5294501 MACS_peak_782 100.24 +chr1 5295225 5295496 MACS_peak_783 170.94 +chr1 5295638 5296068 MACS_peak_784 160.91 +chr1 5296664 5296893 MACS_peak_785 100.06 +chr1 5297035 5297147 MACS_peak_786 100.24 +chr1 5297414 5297652 MACS_peak_787 173.76 +chr1 5298093 5298205 MACS_peak_788 100.24 +chr1 5298450 5298562 MACS_peak_789 100.24 +chr1 5298836 5298948 MACS_peak_790 100.24 +chr1 5299179 5299291 MACS_peak_791 100.24 +chr1 5301534 5302030 MACS_peak_792 123.42 +chr1 5302355 5302467 MACS_peak_793 100.24 +chr1 5303486 5303988 MACS_peak_794 192.69 +chr1 5304193 5304415 MACS_peak_795 100.24 +chr1 5304910 5305054 MACS_peak_796 137.07 +chr1 5305212 5305561 MACS_peak_797 277.50 +chr1 5305849 5305961 MACS_peak_798 100.24 +chr1 5306358 5307242 MACS_peak_799 421.57 +chr1 5307503 5307615 MACS_peak_800 100.24 +chr1 5307966 5308078 MACS_peak_801 100.24 +chr1 5308356 5308796 MACS_peak_802 160.42 +chr1 5308937 5309049 MACS_peak_803 100.24 +chr1 5309978 5310174 MACS_peak_804 213.48 +chr1 5310859 5311560 MACS_peak_805 360.93 +chr1 5312430 5312542 MACS_peak_806 100.24 +chr1 5312774 5313432 MACS_peak_807 220.26 +chr1 5313660 5313837 MACS_peak_808 137.07 +chr1 5314653 5314836 MACS_peak_809 174.88 +chr1 5315019 5315195 MACS_peak_810 137.07 +chr1 5315769 5315897 MACS_peak_811 137.07 +chr1 5316584 5316696 MACS_peak_812 100.24 +chr1 5316832 5316963 MACS_peak_813 137.07 +chr1 5317136 5317248 MACS_peak_814 100.24 +chr1 5317391 5317503 MACS_peak_815 100.24 +chr1 5317762 5317960 MACS_peak_816 137.07 +chr1 5318214 5318326 MACS_peak_817 100.24 +chr1 5318467 5318579 MACS_peak_818 100.24 +chr1 5319598 5319710 MACS_peak_819 100.24 +chr1 5323467 5323847 MACS_peak_820 163.60 +chr1 5324049 5324358 MACS_peak_821 96.16 +chr1 5324608 5325155 MACS_peak_822 225.88 +chr1 5325488 5325600 MACS_peak_823 100.24 +chr1 5325740 5325852 MACS_peak_824 100.24 +chr1 5326235 5326358 MACS_peak_825 137.07 +chr1 5326624 5326736 MACS_peak_826 100.24 +chr1 5327281 5327573 MACS_peak_827 132.62 +chr1 5327763 5327875 MACS_peak_828 100.24 +chr1 5328183 5328407 MACS_peak_829 137.07 +chr1 5328841 5329232 MACS_peak_830 127.55 +chr1 5329875 5330189 MACS_peak_831 95.95 +chr1 5330659 5330843 MACS_peak_832 137.07 +chr1 5331227 5331644 MACS_peak_833 126.43 +chr1 5332229 5332997 MACS_peak_834 148.32 +chr1 5333621 5333919 MACS_peak_835 96.63 +chr1 5336159 5336284 MACS_peak_836 137.07 +chr1 5336624 5336736 MACS_peak_837 100.24 +chr1 5338469 5338837 MACS_peak_838 128.61 +chr1 5341114 5341226 MACS_peak_839 100.24 +chr1 5348682 5349065 MACS_peak_840 199.74 +chr1 5351411 5351523 MACS_peak_841 100.24 +chr1 5353817 5354635 MACS_peak_842 213.65 +chr1 5354853 5354965 MACS_peak_843 100.24 +chr1 5355226 5355738 MACS_peak_844 122.87 +chr1 5356031 5356587 MACS_peak_845 190.03 +chr1 5356826 5356938 MACS_peak_846 100.24 +chr1 5358473 5358620 MACS_peak_847 137.07 +chr1 5359262 5359374 MACS_peak_848 100.24 +chr1 5359830 5360056 MACS_peak_849 100.24 +chr1 5360690 5360802 MACS_peak_850 100.24 +chr1 5361077 5361237 MACS_peak_851 100.24 +chr1 5361530 5361845 MACS_peak_852 131.31 +chr1 5362114 5362226 MACS_peak_853 100.24 +chr1 5362446 5362765 MACS_peak_854 131.09 +chr1 5363772 5363884 MACS_peak_855 100.24 +chr1 5364061 5364281 MACS_peak_856 137.07 +chr1 5364765 5365453 MACS_peak_857 289.45 +chr1 5369402 5369522 MACS_peak_858 137.07 +chr1 5369724 5370212 MACS_peak_859 158.17 +chr1 5370537 5370922 MACS_peak_860 199.60 +chr1 5371214 5371326 MACS_peak_861 100.24 +chr1 5371623 5371735 MACS_peak_862 100.24 +chr1 5372053 5372738 MACS_peak_863 184.59 +chr1 5372983 5373095 MACS_peak_864 100.24 +chr1 5373677 5373936 MACS_peak_865 134.71 +chr1 5374110 5374317 MACS_peak_866 100.24 +chr1 5374621 5374787 MACS_peak_867 100.24 +chr1 5375015 5375148 MACS_peak_868 137.07 +chr1 5375692 5375804 MACS_peak_869 100.24 +chr1 5376645 5376921 MACS_peak_870 97.63 +chr1 5377193 5377305 MACS_peak_871 100.24 +chr1 5377627 5377739 MACS_peak_872 100.24 +chr1 5378171 5378283 MACS_peak_873 100.24 +chr1 5378780 5378892 MACS_peak_874 100.24 +chr1 5379864 5379976 MACS_peak_875 100.24 +chr1 5380338 5380497 MACS_peak_876 100.24 +chr1 5381362 5381897 MACS_peak_877 156.17 +chr1 5382544 5382739 MACS_peak_878 137.07 +chr1 5383063 5383175 MACS_peak_879 100.24 +chr1 5384104 5384571 MACS_peak_880 267.38 +chr1 5384899 5385011 MACS_peak_881 100.24 +chr1 5385907 5386019 MACS_peak_882 100.24 +chr1 5386152 5386562 MACS_peak_883 161.95 +chr1 5386780 5387026 MACS_peak_884 250.17 +chr1 5387186 5387298 MACS_peak_885 100.24 +chr1 5387430 5387542 MACS_peak_886 100.24 +chr1 5388238 5388350 MACS_peak_887 100.24 +chr1 5388677 5388789 MACS_peak_888 100.24 +chr1 5389752 5389864 MACS_peak_889 100.24 +chr1 5390871 5390983 MACS_peak_890 100.24 +chr1 5391768 5391880 MACS_peak_891 100.24 +chr1 5392107 5392219 MACS_peak_892 100.24 +chr1 5392575 5392687 MACS_peak_893 100.24 +chr1 5392911 5393023 MACS_peak_894 100.24 +chr1 5393487 5393599 MACS_peak_895 100.24 +chr1 5393950 5394062 MACS_peak_896 100.24 +chr1 5394309 5394421 MACS_peak_897 100.24 +chr1 5394907 5395019 MACS_peak_898 100.24 +chr1 5395147 5395259 MACS_peak_899 100.24 +chr1 5395472 5395733 MACS_peak_900 134.57 +chr1 5396464 5396791 MACS_peak_901 166.86 +chr1 5397126 5397238 MACS_peak_902 100.24 +chr1 5397681 5397793 MACS_peak_903 100.24 +chr1 5398165 5398319 MACS_peak_904 100.24 +chr1 5399619 5399760 MACS_peak_905 137.07 +chr1 5400650 5401142 MACS_peak_906 265.57 +chr1 5401404 5401516 MACS_peak_907 100.24 +chr1 5401643 5401755 MACS_peak_908 100.24 +chr1 5402151 5402415 MACS_peak_909 98.21 +chr1 5402963 5403143 MACS_peak_910 100.24 +chr1 5403907 5404247 MACS_peak_911 129.98 +chr1 5405321 5405433 MACS_peak_912 100.24 +chr1 5405744 5405856 MACS_peak_913 100.24 +chr1 5407339 5407836 MACS_peak_914 157.77 +chr1 5408061 5408173 MACS_peak_915 100.24 +chr1 5408557 5408669 MACS_peak_916 100.24 +chr1 5408846 5409368 MACS_peak_917 191.67 +chr1 5409651 5409882 MACS_peak_918 174.41 +chr1 5410205 5410317 MACS_peak_919 100.24 +chr1 5410454 5410566 MACS_peak_920 100.24 +chr1 5410745 5410915 MACS_peak_921 100.24 +chr1 5411515 5411627 MACS_peak_922 100.24 +chr1 5411988 5412276 MACS_peak_923 207.16 +chr1 5412450 5412739 MACS_peak_924 169.54 +chr1 5412903 5413063 MACS_peak_925 100.24 +chr1 5413539 5413651 MACS_peak_926 100.24 +chr1 5414865 5414977 MACS_peak_927 100.24 +chr1 5420860 5421109 MACS_peak_928 135.39 +chr1 5428000 5428519 MACS_peak_929 122.63 +chr1 5429035 5429300 MACS_peak_930 134.31 +chr1 5429474 5430067 MACS_peak_931 331.88 +chr1 5430868 5430980 MACS_peak_932 100.24 +chr1 5431368 5431603 MACS_peak_933 99.73 +chr1 5431763 5432040 MACS_peak_934 133.54 +chr1 5432590 5433045 MACS_peak_935 124.92 +chr1 5433978 5434479 MACS_peak_936 123.25 +chr1 5436699 5436811 MACS_peak_937 100.24 +chr1 5439583 5439762 MACS_peak_938 100.24 +chr1 5439969 5440081 MACS_peak_939 100.24 +chr1 5440202 5440466 MACS_peak_940 134.37 +chr1 5442066 5442392 MACS_peak_941 241.61 +chr1 5442655 5442900 MACS_peak_942 135.67 +chr1 5443104 5443663 MACS_peak_943 155.22 +chr1 5444022 5444134 MACS_peak_944 100.24 +chr1 5444854 5444966 MACS_peak_945 100.24 +chr1 5446233 5446411 MACS_peak_946 100.24 +chr1 5446923 5447035 MACS_peak_947 100.24 +chr1 5447953 5448404 MACS_peak_948 268.59 +chr1 5448527 5448801 MACS_peak_949 97.73 +chr1 5448936 5449234 MACS_peak_950 96.63 +chr1 5451111 5451223 MACS_peak_951 100.24 +chr1 5451833 5451945 MACS_peak_952 100.24 +chr1 5452089 5452282 MACS_peak_953 100.24 +chr1 5452539 5452780 MACS_peak_954 135.96 +chr1 5453277 5453389 MACS_peak_955 100.24 +chr1 5453504 5454001 MACS_peak_956 228.79 +chr1 5454325 5454437 MACS_peak_957 100.24 +chr1 5454758 5455004 MACS_peak_958 99.13 +chr1 5455134 5455246 MACS_peak_959 100.24 +chr1 5455945 5456161 MACS_peak_960 174.88 +chr1 5456297 5456409 MACS_peak_961 100.24 +chr1 5456864 5457147 MACS_peak_962 97.31 +chr1 5457642 5457754 MACS_peak_963 100.24 +chr1 5458103 5458215 MACS_peak_964 100.24 +chr1 5460540 5460652 MACS_peak_965 100.24 +chr1 5461820 5461932 MACS_peak_966 100.24 +chr1 5462911 5463023 MACS_peak_967 100.24 +chr1 5470721 5470985 MACS_peak_968 134.37 +chr1 5472485 5472597 MACS_peak_969 100.24 +chr1 5475515 5475779 MACS_peak_970 209.43 +chr1 5476676 5476818 MACS_peak_971 137.07 +chr1 5478224 5478336 MACS_peak_972 100.24 +chr1 5478474 5478586 MACS_peak_973 100.24 +chr1 5478817 5478929 MACS_peak_974 100.24 +chr1 5480909 5481021 MACS_peak_975 100.24 +chr1 5481599 5481711 MACS_peak_976 100.24 +chr1 5482077 5482189 MACS_peak_977 100.24 +chr1 5483535 5483720 MACS_peak_978 137.07 +chr1 5484900 5485245 MACS_peak_979 129.73 +chr1 5485374 5485486 MACS_peak_980 100.24 +chr1 5486127 5486239 MACS_peak_981 100.24 +chr1 5486825 5486937 MACS_peak_982 100.24 +chr1 5487580 5487748 MACS_peak_983 100.24 +chr1 5487864 5488141 MACS_peak_984 170.46 +chr1 5488854 5488966 MACS_peak_985 100.24 +chr1 5492731 5492846 MACS_peak_986 137.07 +chr1 5493221 5493333 MACS_peak_987 100.24 +chr1 5493915 5494069 MACS_peak_988 100.24 +chr1 5496103 5496419 MACS_peak_989 131.25 +chr1 5496817 5497009 MACS_peak_990 137.07 +chr1 5497128 5497240 MACS_peak_991 100.24 +chr1 5497499 5497611 MACS_peak_992 100.24 +chr1 5497727 5498173 MACS_peak_993 160.12 +chr1 5498588 5498967 MACS_peak_994 128.09 +chr1 5501839 5501951 MACS_peak_995 100.24 +chr1 5502127 5502441 MACS_peak_996 95.95 +chr1 5502702 5502889 MACS_peak_997 100.24 +chr1 5503139 5503251 MACS_peak_998 100.24 +chr1 5503416 5503932 MACS_peak_999 122.74 +chr1 5504222 5504334 MACS_peak_1000 100.24 +chr1 5504630 5504773 MACS_peak_1001 137.07 +chr1 5505091 5505493 MACS_peak_1002 127.07 +chr1 5505842 5506053 MACS_peak_1003 100.24 +chr1 5506187 5506366 MACS_peak_1004 137.07 +chr1 5506700 5506812 MACS_peak_1005 100.24 +chr1 5507137 5508211 MACS_peak_1006 205.38 +chr1 5508512 5508959 MACS_peak_1007 160.07 +chr1 5509346 5509458 MACS_peak_1008 100.24 +chr1 5509588 5509700 MACS_peak_1009 100.24 +chr1 5510449 5511245 MACS_peak_1010 427.49 +chr1 5511937 5512049 MACS_peak_1011 100.24 +chr1 5512408 5512787 MACS_peak_1012 237.03 +chr1 5514476 5514635 MACS_peak_1013 100.24 +chr1 5514751 5515081 MACS_peak_1014 130.50 +chr1 5515212 5515324 MACS_peak_1015 100.24 +chr1 5515589 5515853 MACS_peak_1016 134.37 +chr1 5516182 5516294 MACS_peak_1017 100.24 +chr1 5516448 5516560 MACS_peak_1018 100.24 +chr1 5522530 5522642 MACS_peak_1019 100.24 +chr1 5522808 5523114 MACS_peak_1020 96.29 +chr1 5523747 5523859 MACS_peak_1021 100.24 +chr1 5524091 5524648 MACS_peak_1022 155.30 +chr1 5525817 5525929 MACS_peak_1023 100.24 +chr1 5526129 5526352 MACS_peak_1024 100.24 +chr1 5526994 5527106 MACS_peak_1025 100.24 +chr1 5527307 5527419 MACS_peak_1026 100.24 +chr1 5527948 5528060 MACS_peak_1027 100.24 +chr1 5528479 5528591 MACS_peak_1028 100.24 +chr1 5528843 5528955 MACS_peak_1029 100.24 +chr1 5529535 5529795 MACS_peak_1030 98.41 +chr1 5530073 5530501 MACS_peak_1031 125.98 +chr1 5530662 5530801 MACS_peak_1032 137.07 +chr1 5530933 5531145 MACS_peak_1033 100.24 +chr1 5532316 5532575 MACS_peak_1034 209.93 +chr1 5532814 5533414 MACS_peak_1035 223.07 +chr1 5533683 5534046 MACS_peak_1036 238.34 +chr1 5534750 5534862 MACS_peak_1037 100.24 +chr1 5535654 5536031 MACS_peak_1038 128.19 +chr1 5539337 5539449 MACS_peak_1039 100.24 +chr1 5539958 5540105 MACS_peak_1040 174.88 +chr1 5540372 5540520 MACS_peak_1041 137.07 +chr1 5540857 5541254 MACS_peak_1042 162.65 +chr1 5541543 5541655 MACS_peak_1043 100.24 +chr1 5547312 5547424 MACS_peak_1044 100.24 +chr1 5548151 5548263 MACS_peak_1045 100.24 +chr1 5548760 5549292 MACS_peak_1046 226.73 +chr1 5549828 5549972 MACS_peak_1047 137.07 +chr1 5550175 5550306 MACS_peak_1048 137.07 +chr1 5550522 5550679 MACS_peak_1049 100.24 +chr1 5550864 5551382 MACS_peak_1050 156.87 +chr1 5552871 5552983 MACS_peak_1051 100.24 +chr1 5555738 5555850 MACS_peak_1052 100.24 +chr1 5559490 5559602 MACS_peak_1053 100.24 +chr1 5560846 5560958 MACS_peak_1054 100.24 +chr1 5561340 5561521 MACS_peak_1055 100.24 +chr1 5563505 5563769 MACS_peak_1056 98.21 +chr1 5564533 5564700 MACS_peak_1057 100.24 +chr1 5564912 5565024 MACS_peak_1058 100.24 +chr1 5565259 5565371 MACS_peak_1059 100.24 +chr1 5568363 5568657 MACS_peak_1060 283.46 +chr1 5569291 5570044 MACS_peak_1061 216.17 +chr1 5570260 5570902 MACS_peak_1062 292.15 +chr1 5571279 5571615 MACS_peak_1063 130.19 +chr1 5571758 5572146 MACS_peak_1064 236.32 +chr1 5572441 5572553 MACS_peak_1065 100.24 +chr1 5572747 5572859 MACS_peak_1066 100.24 +chr1 5573400 5573512 MACS_peak_1067 100.24 +chr1 5576223 5576419 MACS_peak_1068 100.24 +chr1 5576544 5576662 MACS_peak_1069 137.07 +chr1 5576892 5577241 MACS_peak_1070 129.53 +chr1 5577515 5578153 MACS_peak_1071 256.54 +chr1 5578298 5578410 MACS_peak_1072 100.24 +chr1 5578808 5578920 MACS_peak_1073 100.24 +chr1 5579210 5579554 MACS_peak_1074 129.78 +chr1 5579672 5580062 MACS_peak_1075 199.26 +chr1 5580481 5580593 MACS_peak_1076 100.24 +chr1 5580882 5580994 MACS_peak_1077 100.24 +chr1 5581303 5581626 MACS_peak_1078 241.89 +chr1 5581877 5581989 MACS_peak_1079 100.24 +chr1 5582232 5582417 MACS_peak_1080 100.24 +chr1 5582575 5583094 MACS_peak_1081 122.63 +chr1 5583521 5583633 MACS_peak_1082 100.24 +chr1 5583818 5583930 MACS_peak_1083 100.24 +chr1 5584211 5584323 MACS_peak_1084 100.24 +chr1 5584502 5584788 MACS_peak_1085 97.17 +chr1 5585486 5585847 MACS_peak_1086 164.71 +chr1 5586024 5586188 MACS_peak_1087 174.88 +chr1 5586310 5586426 MACS_peak_1088 137.07 +chr1 5586843 5586955 MACS_peak_1089 100.24 +chr1 5587182 5587294 MACS_peak_1090 100.24 +chr1 5587715 5588020 MACS_peak_1091 131.87 +chr1 5588165 5588277 MACS_peak_1092 100.24 +chr1 5588680 5588894 MACS_peak_1093 174.88 +chr1 5589048 5589314 MACS_peak_1094 98.11 +chr1 5589639 5589751 MACS_peak_1095 100.24 +chr1 5589901 5590358 MACS_peak_1096 231.34 +chr1 5591315 5591427 MACS_peak_1097 100.24 +chr1 5591562 5591674 MACS_peak_1098 100.24 +chr1 5591879 5591991 MACS_peak_1099 100.24 +chr1 5592196 5592429 MACS_peak_1100 99.84 +chr1 5593248 5594359 MACS_peak_1101 588.30 +chr1 5594491 5594708 MACS_peak_1102 174.88 +chr1 5595151 5595263 MACS_peak_1103 100.24 +chr1 5595498 5595820 MACS_peak_1104 130.92 +chr1 5596027 5596139 MACS_peak_1105 100.24 +chr1 5596276 5596388 MACS_peak_1106 100.24 +chr1 5596667 5596945 MACS_peak_1107 208.08 +chr1 5597235 5597476 MACS_peak_1108 99.40 +chr1 5598124 5598263 MACS_peak_1109 137.07 +chr1 5598532 5598644 MACS_peak_1110 100.24 +chr1 5598989 5599453 MACS_peak_1111 159.26 +chr1 5599963 5600126 MACS_peak_1112 174.88 +chr1 5600438 5600611 MACS_peak_1113 100.24 +chr1 5601284 5601731 MACS_peak_1114 125.23 +chr1 5602492 5602639 MACS_peak_1115 137.07 +chr1 5603011 5603123 MACS_peak_1116 100.24 +chr1 5603421 5603960 MACS_peak_1117 156.01 +chr1 5604580 5604898 MACS_peak_1118 95.79 +chr1 5605109 5605221 MACS_peak_1119 100.24 +chr1 5605645 5605886 MACS_peak_1120 99.40 +chr1 5606332 5606831 MACS_peak_1121 192.84 +chr1 5607289 5607401 MACS_peak_1122 100.24 +chr1 5607640 5607752 MACS_peak_1123 100.24 +chr1 5608156 5608359 MACS_peak_1124 100.24 +chr1 5609092 5609220 MACS_peak_1125 137.07 +chr1 5609679 5609791 MACS_peak_1126 100.24 +chr1 5610548 5610660 MACS_peak_1127 100.24 +chr1 5610980 5611132 MACS_peak_1128 100.24 +chr1 5611284 5611396 MACS_peak_1129 100.24 +chr1 5611566 5611772 MACS_peak_1130 100.24 +chr1 5611896 5612157 MACS_peak_1131 98.36 +chr1 5612291 5612403 MACS_peak_1132 100.24 +chr1 5612549 5612718 MACS_peak_1133 174.88 +chr1 5612859 5613143 MACS_peak_1134 133.11 +chr1 5613560 5613672 MACS_peak_1135 100.24 +chr1 5614561 5615373 MACS_peak_1136 282.97 +chr1 5615704 5615816 MACS_peak_1137 100.24 +chr1 5616141 5616253 MACS_peak_1138 100.24 +chr1 5616372 5616484 MACS_peak_1139 100.24 +chr1 5616668 5617219 MACS_peak_1140 335.07 +chr1 5617497 5617795 MACS_peak_1141 96.63 +chr1 5619893 5620086 MACS_peak_1142 100.24 +chr1 5620435 5620547 MACS_peak_1143 100.24 +chr1 5621379 5622034 MACS_peak_1144 220.40 +chr1 5624571 5624683 MACS_peak_1145 100.24 +chr1 5625232 5625344 MACS_peak_1146 100.24 +chr1 5627078 5627190 MACS_peak_1147 100.24 +chr1 5632017 5632129 MACS_peak_1148 100.24 +chr1 5632376 5632652 MACS_peak_1149 170.54 +chr1 5633321 5633535 MACS_peak_1150 137.07 +chr1 5633696 5633881 MACS_peak_1151 100.24 +chr1 5634469 5634687 MACS_peak_1152 100.24 +chr1 5635062 5635329 MACS_peak_1153 98.06 +chr1 5635461 5635573 MACS_peak_1154 100.24 +chr1 5635728 5635840 MACS_peak_1155 100.24 +chr1 5636596 5636789 MACS_peak_1156 100.24 +chr1 5637075 5637187 MACS_peak_1157 100.24 +chr1 5637607 5637719 MACS_peak_1158 100.24 +chr1 5640953 5641065 MACS_peak_1159 100.24 +chr1 5643184 5643361 MACS_peak_1160 100.24 +chr1 5644450 5644562 MACS_peak_1161 100.24 +chr1 5646326 5646650 MACS_peak_1162 130.82 +chr1 5646766 5647194 MACS_peak_1163 125.98 +chr1 5647474 5647766 MACS_peak_1164 132.62 +chr1 5648437 5649089 MACS_peak_1165 364.39 +chr1 5649411 5650167 MACS_peak_1166 467.44 +chr1 5650744 5650944 MACS_peak_1167 137.07 +chr1 5651395 5651820 MACS_peak_1168 197.02 +chr1 5652003 5652323 MACS_peak_1169 167.33 +chr1 5652795 5653010 MACS_peak_1170 137.07 +chr1 5653365 5653689 MACS_peak_1171 318.88 +chr1 5653877 5653989 MACS_peak_1172 100.24 +chr1 5654231 5654343 MACS_peak_1173 100.24 +chr1 5654571 5654866 MACS_peak_1174 96.76 +chr1 5655769 5656176 MACS_peak_1175 198.15 +chr1 5656312 5656424 MACS_peak_1176 100.24 +chr1 5657271 5657383 MACS_peak_1177 100.24 +chr1 5657651 5657988 MACS_peak_1178 166.21 +chr1 5658525 5658637 MACS_peak_1179 100.24 +chr1 5659194 5659308 MACS_peak_1180 137.07 +chr1 5660375 5660575 MACS_peak_1181 137.07 +chr1 5660781 5660893 MACS_peak_1182 100.24 +chr1 5661327 5661439 MACS_peak_1183 100.24 +chr1 5662504 5662697 MACS_peak_1184 137.07 +chr1 5663691 5663885 MACS_peak_1185 137.07 +chr1 5664582 5664750 MACS_peak_1186 100.24 +chr1 5665076 5665188 MACS_peak_1187 100.24 +chr1 5665895 5666007 MACS_peak_1188 100.24 +chr1 5666448 5666930 MACS_peak_1189 193.75 +chr1 5667751 5667934 MACS_peak_1190 100.24 +chr1 5674057 5674169 MACS_peak_1191 100.24 +chr1 5675063 5675175 MACS_peak_1192 100.24 +chr1 5676274 5676386 MACS_peak_1193 100.24 +chr1 5676599 5676711 MACS_peak_1194 100.24 +chr1 5677228 5677340 MACS_peak_1195 100.24 +chr1 5677740 5677852 MACS_peak_1196 100.24 +chr1 5679022 5679667 MACS_peak_1197 291.97 +chr1 5680026 5681034 MACS_peak_1198 240.66 +chr1 5682911 5683023 MACS_peak_1199 100.24 +chr1 5688032 5688144 MACS_peak_1200 100.24 +chr1 5688335 5688657 MACS_peak_1201 130.92 +chr1 5688801 5688913 MACS_peak_1202 100.24 +chr1 5689087 5689348 MACS_peak_1203 98.36 +chr1 5689475 5689587 MACS_peak_1204 100.24 +chr1 5689771 5689883 MACS_peak_1205 100.24 +chr1 5690261 5690373 MACS_peak_1206 100.24 +chr1 5690750 5690873 MACS_peak_1207 137.07 +chr1 5694742 5695180 MACS_peak_1208 160.51 +chr1 5695333 5695675 MACS_peak_1209 129.88 +chr1 5696080 5696192 MACS_peak_1210 100.24 +chr1 5696612 5697345 MACS_peak_1211 251.72 +chr1 5697961 5698073 MACS_peak_1212 100.24 +chr1 5698235 5698383 MACS_peak_1213 137.07 +chr1 5698832 5699021 MACS_peak_1214 100.24 +chr1 5699479 5699591 MACS_peak_1215 100.24 +chr1 5700029 5700141 MACS_peak_1216 100.24 +chr1 5700387 5700503 MACS_peak_1217 137.07 +chr1 5703736 5703848 MACS_peak_1218 100.24 +chr1 5704571 5704683 MACS_peak_1219 100.24 +chr1 5704979 5705219 MACS_peak_1220 136.03 +chr1 5705728 5705840 MACS_peak_1221 100.24 +chr1 5706213 5706482 MACS_peak_1222 247.45 +chr1 5706879 5706991 MACS_peak_1223 100.24 +chr1 5707211 5707414 MACS_peak_1224 100.24 +chr1 5707733 5707955 MACS_peak_1225 100.24 +chr1 5708418 5708530 MACS_peak_1226 100.24 +chr1 5708711 5708823 MACS_peak_1227 100.24 +chr1 5709009 5709168 MACS_peak_1228 100.24 +chr1 5709626 5709738 MACS_peak_1229 100.24 +chr1 5710175 5710287 MACS_peak_1230 100.24 +chr1 5711491 5711603 MACS_peak_1231 100.24 +chr1 5712452 5712913 MACS_peak_1232 159.40 +chr1 5713590 5713702 MACS_peak_1233 100.24 +chr1 5714277 5714835 MACS_peak_1234 189.93 +chr1 5715628 5715793 MACS_peak_1235 100.24 +chr1 5715919 5716031 MACS_peak_1236 100.24 +chr1 5716150 5716384 MACS_peak_1237 174.12 +chr1 5717000 5717112 MACS_peak_1238 100.24 +chr1 5717383 5717774 MACS_peak_1239 127.55 +chr1 5718298 5718531 MACS_peak_1240 136.54 +chr1 5718754 5719002 MACS_peak_1241 172.86 +chr1 5719627 5719739 MACS_peak_1242 100.24 +chr1 5720578 5720690 MACS_peak_1243 100.24 +chr1 5721523 5721843 MACS_peak_1244 95.71 +chr1 5722221 5722388 MACS_peak_1245 100.24 +chr1 5722739 5722851 MACS_peak_1246 100.24 +chr1 5723148 5723403 MACS_peak_1247 134.98 +chr1 5724342 5724566 MACS_peak_1248 100.24 +chr1 5725453 5725597 MACS_peak_1249 137.07 +chr1 5725942 5726075 MACS_peak_1250 137.07 +chr1 5726202 5726647 MACS_peak_1251 306.48 +chr1 5726801 5726913 MACS_peak_1252 100.24 +chr1 5727303 5727415 MACS_peak_1253 100.24 +chr1 5727541 5727720 MACS_peak_1254 213.48 +chr1 5728015 5728127 MACS_peak_1255 100.24 +chr1 5728661 5728922 MACS_peak_1256 98.36 +chr1 5729591 5729703 MACS_peak_1257 100.24 +chr1 5729971 5730118 MACS_peak_1258 137.07 +chr1 5735097 5735209 MACS_peak_1259 100.24 +chr1 5738165 5738277 MACS_peak_1260 100.24 +chr1 5741886 5742013 MACS_peak_1261 137.07 +chr1 5742222 5742493 MACS_peak_1262 133.92 +chr1 5742624 5742892 MACS_peak_1263 98.02 +chr1 5743479 5743591 MACS_peak_1264 100.24 +chr1 5743802 5743943 MACS_peak_1265 137.07 +chr1 5744327 5745001 MACS_peak_1266 185.01 +chr1 5745544 5746174 MACS_peak_1267 221.59 +chr1 5746482 5747182 MACS_peak_1268 218.38 +chr1 5747751 5747863 MACS_peak_1269 100.24 +chr1 5749480 5749592 MACS_peak_1270 100.24 diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_neg_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_2_neg_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,59 @@ +#negative peaks file +#chr start end length summit tags -10*log10(pvalue) fold_enrichment +chr1 3012338 3012474 136 69 3 79.72 265.54 +chr1 3012631 3012751 120 61 3 79.72 265.54 +chr1 3055826 3056120 294 96 9 59.49 18.22 +chr1 3066934 3067568 634 101 10 53.35 18.44 +chr1 3076059 3076339 280 112 6 58.24 29.50 +chr1 3092687 3093270 583 344 11 50.81 10.32 +chr1 3114123 3114523 400 107 10 51.47 11.06 +chr1 3125324 3126255 931 573 13 65.69 12.07 +chr1 3126473 3127174 701 249 11 65.43 13.28 +chr1 3127353 3127879 526 265 14 110.59 22.13 +chr1 3195224 3195844 620 395 13 56.61 13.28 +chr1 3228283 3228748 465 388 6 50.25 26.55 +chr1 3275975 3276467 492 404 9 55.17 15.39 +chr1 3285007 3286005 998 891 18 66.19 11.06 +chr1 3312699 3313743 1044 204 21 60.12 11.06 +chr1 3446632 3447508 876 176 14 61.26 14.75 +chr1 3468402 3469436 1034 109 18 50.75 7.08 +chr1 3474772 3476374 1602 960 22 66.92 12.29 +chr1 3514508 3515086 578 110 13 59.90 11.06 +chr1 3517009 3518094 1085 84 14 50.75 11.80 +chr1 3599829 3601141 1312 109 19 65.77 10.41 +chr1 3605828 3605951 123 62 4 52.20 18.63 +chr1 3606596 3607433 837 548 10 66.22 27.23 +chr1 3613851 3614116 265 103 6 57.63 34.04 +chr1 3614432 3615882 1450 85 15 63.55 13.28 +chr1 3617465 3617784 319 211 9 51.03 11.06 +chr1 3640315 3641949 1634 273 32 81.39 10.68 +chr1 3647349 3648562 1213 411 19 67.14 9.83 +chr1 3735801 3736852 1051 878 17 73.61 14.75 +chr1 3796005 3796544 539 65 5 54.89 44.26 +chr1 3797371 3797763 392 70 6 54.44 26.55 +chr1 3835421 3835673 252 171 6 53.74 22.13 +chr1 3856581 3857561 980 110 19 52.84 9.48 +chr1 3968246 3968621 375 85 7 60.72 34.04 +chr1 3970428 3970718 290 69 5 56.15 50.58 +chr1 4034953 4036094 1141 465 15 66.64 18.44 +chr1 4051823 4055268 3445 669 46 119.08 9.32 +chr1 4099917 4100882 965 256 18 84.48 11.39 +chr1 4112353 4113269 916 72 15 53.99 9.32 +chr1 4139620 4140296 676 399 14 71.23 11.06 +chr1 4191034 4191488 454 386 9 51.16 15.81 +chr1 4191774 4192345 571 102 10 51.50 12.64 +chr1 4201259 4202176 917 651 13 64.28 19.24 +chr1 4218597 4219458 861 460 16 53.64 5.77 +chr1 4223608 4224231 623 472 14 78.93 14.75 +chr1 4238528 4239382 854 90 14 54.69 15.12 +chr1 4283406 4284196 790 400 11 60.42 22.13 +chr1 4368609 4369824 1215 504 19 72.89 10.75 +chr1 4382657 4385390 2733 1297 36 97.80 12.10 +chr1 4439048 4440167 1119 927 19 80.31 13.83 +chr1 4447108 4448669 1561 1375 31 62.31 7.54 +chr1 4462162 4466719 4557 4366 75 90.49 8.30 +chr1 4479282 4480091 809 700 19 60.40 10.33 +chr1 4568704 4569556 852 319 25 69.71 8.62 +chr1 4596926 4597745 819 449 17 51.74 9.48 +chr1 4636007 4637827 1820 110 30 51.27 8.57 +chr1 4646136 4647867 1731 101 28 53.47 7.38 diff -r 49961332adb6 -r e9de35947c06 test-data/macs_test_2_peaks_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_test_2_peaks_out.interval Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,1289 @@ +#peaks file +# This file is generated by MACS +# ARGUMENTS LIST: +# name = MACS_in_Galaxy +# format = BED +# ChIP-seq file = /galaxy/home/dan/central/database/files/000/dataset_404.dat +# control file = /galaxy/home/dan/central/database/files/000/dataset_405.dat +# effective genome size = 2.70e+09 +# tag size = 36 +# band width = 300 +# model fold = 13 +# pvalue cutoff = 1.00e-05 +# Ranges for calculating regional lambda are : peak_region,1000,5000,10000 +# unique tags in treatment: 9898 +# total tags in treatment: 10000 +# unique tags in control: 9896 +# total tags in control: 10000 +# d = 113 +#chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%) +chr1 3138857 3139271 414 95 6 53.08 35.39 3.55 +chr1 4133899 4134700 801 157 27 51.91 9.92 3.70 +chr1 4323670 4324367 697 306 49 272.01 29.81 0.00 +chr1 4336486 4337946 1460 1216 65 228.35 32.00 0.00 +chr1 4407086 4409120 2034 1133 105 300.46 29.27 0.00 +chr1 4507832 4508710 878 245 44 161.74 18.90 0.00 +chr1 4657704 4658572 868 775 9 280.37 7242.01 0.00 +chr1 4658705 4659021 316 110 4 131.25 4828.01 0.00 +chr1 4659147 4660581 1434 844 15 463.08 7242.01 0.00 +chr1 4661156 4661317 161 81 4 174.88 9656.01 0.00 +chr1 4661505 4661617 112 57 2 100.24 4828.01 0.17 +chr1 4661790 4662463 673 287 7 219.58 4828.01 0.00 +chr1 4662710 4663434 724 623 12 395.94 9656.01 0.00 +chr1 4664135 4664430 295 64 5 169.10 7242.01 0.00 +chr1 4665001 4665113 112 57 2 100.24 4828.01 0.17 +chr1 4665839 4666425 586 475 10 332.40 12070.02 0.00 +chr1 4666581 4666693 112 57 2 100.24 4828.01 0.17 +chr1 4666840 4666981 141 71 4 174.88 9656.01 0.00 +chr1 4667600 4667712 112 57 2 100.24 4828.01 0.17 +chr1 4668711 4669005 294 75 5 169.17 7242.01 0.00 +chr1 4669126 4669238 112 57 2 100.24 4828.01 0.17 +chr1 4669537 4669752 215 108 5 174.88 12070.02 0.00 +chr1 4669936 4670048 112 57 2 100.24 4828.01 0.17 +chr1 4670216 4670449 233 97 6 212.68 12070.02 0.00 +chr1 4673856 4674051 195 98 4 137.07 9656.01 0.00 +chr1 4674349 4674478 129 65 3 137.07 7242.01 0.00 +chr1 4675027 4675152 125 63 3 137.07 7242.01 0.00 +chr1 4676227 4676339 112 57 2 100.24 4828.01 0.17 +chr1 4676511 4676623 112 57 2 100.24 4828.01 0.17 +chr1 4676954 4677151 197 99 3 100.24 7242.01 0.17 +chr1 4677646 4677758 112 57 2 100.24 4828.01 0.17 +chr1 4678360 4678472 112 57 2 100.24 4828.01 0.17 +chr1 4678659 4679136 477 307 7 230.04 7242.01 0.00 +chr1 4679439 4679551 112 57 2 100.24 4828.01 0.17 +chr1 4680106 4680523 417 103 5 126.43 4828.01 0.00 +chr1 4680822 4680934 112 57 2 100.24 4828.01 0.17 +chr1 4681075 4682050 975 104 8 241.81 4828.01 0.00 +chr1 4682229 4682387 158 80 3 100.24 7242.01 0.17 +chr1 4682594 4682706 112 57 2 100.24 4828.01 0.17 +chr1 4683158 4683270 112 57 2 100.24 4828.01 0.17 +chr1 4683473 4683585 112 57 2 100.24 4828.01 0.17 +chr1 4683832 4683944 112 57 2 100.24 4828.01 0.17 +chr1 4684591 4684775 184 93 3 100.24 7242.01 0.17 +chr1 4685292 4685404 112 57 2 100.24 4828.01 0.17 +chr1 4685810 4686198 388 75 4 127.69 4828.01 0.00 +chr1 4686493 4686605 112 57 2 100.24 4828.01 0.17 +chr1 4686818 4686930 112 57 2 100.24 4828.01 0.17 +chr1 4687387 4687499 112 57 2 100.24 4828.01 0.17 +chr1 4687692 4687902 210 106 5 174.88 12070.02 0.00 +chr1 4688181 4688790 609 96 8 258.16 9656.01 0.00 +chr1 4689101 4689557 456 250 7 231.41 9656.01 0.00 +chr1 4690039 4690151 112 57 2 100.24 4828.01 0.17 +chr1 4690290 4690402 112 57 2 100.24 4828.01 0.17 +chr1 4690780 4690907 127 64 3 137.07 7242.01 0.00 +chr1 4691478 4692335 857 509 10 315.89 7242.01 0.00 +chr1 4692464 4692768 304 67 4 131.92 7242.01 0.00 +chr1 4693243 4693751 508 307 7 228.13 9656.01 0.00 +chr1 4694306 4694418 112 57 2 100.24 4828.01 0.17 +chr1 4694738 4695016 278 75 5 170.38 9656.01 0.00 +chr1 4695207 4695378 171 86 3 100.24 7242.01 0.17 +chr1 4695503 4696600 1097 535 12 374.29 7242.01 0.00 +chr1 4696903 4697015 112 57 2 100.24 4828.01 0.17 +chr1 4697569 4697912 343 106 7 240.07 12070.02 0.00 +chr1 4698224 4698395 171 86 3 100.24 7242.01 0.17 +chr1 4698790 4698904 114 58 3 137.07 7242.01 0.00 +chr1 4699223 4699430 207 104 4 137.07 9656.01 0.00 +chr1 4699642 4699754 112 57 2 100.24 4828.01 0.17 +chr1 4700457 4700569 112 57 2 100.24 4828.01 0.17 +chr1 4700853 4700965 112 57 2 100.24 4828.01 0.17 +chr1 4708474 4708898 424 57 4 126.15 4828.01 0.00 +chr1 4709426 4709741 315 102 5 167.67 9656.01 0.00 +chr1 4709925 4710127 202 102 4 137.07 9656.01 0.00 +chr1 4710465 4710577 112 57 2 100.24 4828.01 0.17 +chr1 4710812 4711277 465 111 6 194.68 7242.01 0.00 +chr1 4711462 4711762 300 102 4 132.15 4828.01 0.00 +chr1 4712202 4712479 277 57 3 97.58 4828.01 0.24 +chr1 4712673 4713163 490 111 10 340.17 9656.01 0.00 +chr1 4713659 4714656 997 230 13 414.78 7242.01 0.00 +chr1 4714840 4715470 630 83 7 221.59 7242.01 0.00 +chr1 4715671 4715783 112 57 2 100.24 4828.01 0.17 +chr1 4715908 4716811 903 824 16 530.04 12070.02 0.00 +chr1 4717318 4717430 112 57 2 100.24 4828.01 0.17 +chr1 4717789 4718230 441 103 7 232.43 12070.02 0.00 +chr1 4718990 4719236 246 57 3 99.13 4828.01 0.16 +chr1 4719718 4719830 112 57 2 100.24 4828.01 0.17 +chr1 4720276 4720388 112 57 2 100.24 4828.01 0.17 +chr1 4721061 4721173 112 57 2 100.24 4828.01 0.17 +chr1 4721620 4721782 162 82 3 100.24 7242.01 0.17 +chr1 4722229 4722341 112 57 2 100.24 4828.01 0.17 +chr1 4723262 4723374 112 57 2 100.24 4828.01 0.17 +chr1 4724496 4724608 112 57 2 100.24 4828.01 0.17 +chr1 4726179 4726291 112 57 2 100.24 4828.01 0.17 +chr1 4726472 4727091 619 82 6 187.23 7242.01 0.00 +chr1 4727268 4727705 437 66 6 196.30 7242.01 0.00 +chr1 4727871 4727983 112 57 2 100.24 4828.01 0.17 +chr1 4728976 4729088 112 57 2 100.24 4828.01 0.17 +chr1 4729473 4729611 138 70 3 137.07 7242.01 0.00 +chr1 4729954 4730093 139 70 3 137.07 7242.01 0.00 +chr1 4730636 4730805 169 85 3 100.24 7242.01 0.17 +chr1 4730936 4731305 369 111 5 164.24 9656.01 0.00 +chr1 4731799 4732585 786 443 11 355.47 7242.01 0.00 +chr1 4733192 4733304 112 57 2 100.24 4828.01 0.17 +chr1 4733710 4733831 121 61 3 137.07 7242.01 0.00 +chr1 4734062 4734891 829 75 11 352.92 9656.01 0.00 +chr1 4735075 4735290 215 108 4 137.07 9656.01 0.00 +chr1 4735523 4736190 667 236 7 185.28 4828.01 0.00 +chr1 4736399 4737184 785 80 11 355.53 9656.01 0.00 +chr1 4737395 4737601 206 104 4 137.07 9656.01 0.00 +chr1 4737973 4738425 452 188 7 231.68 7242.01 0.00 +chr1 4738796 4739212 416 311 6 197.58 7242.01 0.00 +chr1 4739379 4739491 112 57 2 100.24 4828.01 0.17 +chr1 4739612 4740720 1108 105 18 588.51 9656.01 0.00 +chr1 4741405 4741655 250 80 4 135.32 7242.01 0.00 +chr1 4741998 4742300 302 79 4 132.04 4828.01 0.00 +chr1 4742829 4742952 123 62 3 137.07 7242.01 0.00 +chr1 4743079 4743327 248 101 4 135.46 4828.01 0.00 +chr1 4743612 4744566 954 97 14 453.30 12070.02 0.00 +chr1 4744719 4745224 505 260 8 264.66 7242.01 0.00 +chr1 4745398 4745786 388 301 8 236.32 9656.01 0.00 +chr1 4746034 4746316 282 112 5 170.07 9656.01 0.00 +chr1 4747206 4748408 1202 316 15 474.57 9656.01 0.00 +chr1 4748814 4748926 112 57 2 100.24 4828.01 0.17 +chr1 4749222 4749334 112 57 2 100.24 4828.01 0.17 +chr1 4749686 4750054 368 97 8 275.66 12070.02 0.00 +chr1 4750335 4750697 362 79 5 164.65 7242.01 0.00 +chr1 4750863 4751682 819 109 8 247.87 4828.01 0.00 +chr1 4751853 4752428 575 78 6 189.15 7242.01 0.00 +chr1 4752581 4753611 1030 565 13 412.95 9656.01 0.00 +chr1 4754241 4754864 623 233 10 329.74 9656.01 0.00 +chr1 4755088 4755200 112 57 2 100.24 4828.01 0.17 +chr1 4755722 4756029 307 100 6 205.50 12070.02 0.00 +chr1 4756768 4756880 112 57 2 100.24 4828.01 0.17 +chr1 4757199 4758615 1416 753 18 569.34 7242.01 0.00 +chr1 4758753 4762214 3461 1125 247 3100.00 217260.30 0.00 +chr1 4763207 4763319 112 57 2 100.24 4828.01 0.17 +chr1 4763614 4763726 112 57 2 100.24 4828.01 0.17 +chr1 4763998 4764322 324 233 10 358.13 14484.02 0.00 +chr1 4764568 4764850 282 62 4 133.23 7242.01 0.00 +chr1 4765104 4765765 661 112 9 291.01 12070.02 0.00 +chr1 4765892 4766067 175 88 3 100.24 7242.01 0.17 +chr1 4766232 4766420 188 95 3 100.24 7242.01 0.17 +chr1 4766539 4767148 609 171 11 367.65 14484.02 0.00 +chr1 4767417 4767529 112 57 2 100.24 4828.01 0.17 +chr1 4768245 4768357 112 57 2 100.24 4828.01 0.17 +chr1 4768587 4768870 283 99 5 170.00 9656.01 0.00 +chr1 4768989 4769272 283 104 4 133.17 4828.01 0.00 +chr1 4769463 4769684 221 111 5 174.88 12070.02 0.00 +chr1 4769861 4770236 375 287 6 200.29 7242.01 0.00 +chr1 4770689 4771270 581 256 7 224.05 7242.01 0.00 +chr1 4771393 4772502 1109 197 49 1799.39 57936.08 0.00 +chr1 4772633 4772916 283 95 4 133.17 7242.01 0.00 +chr1 4773121 4773284 163 82 3 100.24 7242.01 0.17 +chr1 4773476 4773614 138 70 3 137.07 7242.01 0.00 +chr1 4773827 4774279 452 84 5 159.83 7242.01 0.00 +chr1 4774510 4774622 112 57 2 100.24 4828.01 0.17 +chr1 4775041 4775694 653 100 9 291.49 12070.02 0.00 +chr1 4775832 4775944 112 57 2 100.24 4828.01 0.17 +chr1 4776166 4776310 144 73 3 137.07 7242.01 0.00 +chr1 4776506 4776851 345 276 5 165.70 7242.01 0.00 +chr1 4777100 4777321 221 111 4 137.07 9656.01 0.00 +chr1 4777505 4777617 112 57 2 100.24 4828.01 0.17 +chr1 4777764 4778298 534 84 5 156.21 4828.01 0.00 +chr1 4778680 4778792 112 57 2 100.24 4828.01 0.17 +chr1 4779265 4779377 112 57 2 100.24 4828.01 0.17 +chr1 4780814 4780926 112 57 2 100.24 4828.01 0.17 +chr1 4781238 4781436 198 100 4 137.07 9656.01 0.00 +chr1 4781600 4781712 112 57 2 100.24 4828.01 0.17 +chr1 4784249 4784487 238 164 5 173.76 7242.01 0.00 +chr1 4784800 4784912 112 57 2 100.24 4828.01 0.17 +chr1 4785500 4785612 112 57 2 100.24 4828.01 0.17 +chr1 4786820 4787357 537 358 7 226.44 4828.01 0.00 +chr1 4787570 4787682 112 57 2 100.24 4828.01 0.17 +chr1 4789440 4789978 538 100 8 262.47 7242.01 0.00 +chr1 4790257 4790424 167 84 3 100.24 7242.01 0.17 +chr1 4790723 4791308 585 104 7 223.84 12070.02 0.00 +chr1 4791871 4792641 770 664 12 392.73 14484.02 0.00 +chr1 4792756 4793323 567 109 6 189.52 7242.01 0.00 +chr1 4794493 4794929 436 254 7 232.77 9656.01 0.00 +chr1 4795046 4795357 311 89 4 131.53 4828.01 0.00 +chr1 4795495 4795607 112 57 2 100.24 4828.01 0.17 +chr1 4796218 4796432 214 108 5 174.88 12070.02 0.00 +chr1 4796841 4796953 112 57 2 100.24 4828.01 0.17 +chr1 4797267 4797499 232 57 3 99.89 4828.01 0.17 +chr1 4797910 4798022 112 57 2 100.24 4828.01 0.17 +chr1 4799151 4799263 112 57 2 100.24 4828.01 0.17 +chr1 4799518 4800266 748 108 8 216.37 7242.01 0.00 +chr1 4800415 4800527 112 57 2 100.24 4828.01 0.17 +chr1 4800989 4801101 112 57 2 100.24 4828.01 0.17 +chr1 4801344 4802288 944 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+chr1 5718754 5719002 248 96 5 172.86 9656.01 0.00 +chr1 5719627 5719739 112 57 2 100.24 4828.01 0.17 +chr1 5720578 5720690 112 57 2 100.24 4828.01 0.17 +chr1 5721523 5721843 320 57 3 95.71 4828.01 0.24 +chr1 5722221 5722388 167 84 3 100.24 7242.01 0.17 +chr1 5722739 5722851 112 57 2 100.24 4828.01 0.17 +chr1 5723148 5723403 255 105 4 134.98 4828.01 0.00 +chr1 5724342 5724566 224 57 3 100.24 4828.01 0.17 +chr1 5725453 5725597 144 73 3 137.07 7242.01 0.00 +chr1 5725942 5726075 133 67 3 137.07 7242.01 0.00 +chr1 5726202 5726647 445 349 9 306.48 12070.02 0.00 +chr1 5726801 5726913 112 57 2 100.24 4828.01 0.17 +chr1 5727303 5727415 112 57 2 100.24 4828.01 0.17 +chr1 5727541 5727720 179 90 5 213.48 12070.02 0.00 +chr1 5728015 5728127 112 57 2 100.24 4828.01 0.17 +chr1 5728661 5728922 261 57 3 98.36 4828.01 0.16 +chr1 5729591 5729703 112 57 2 100.24 4828.01 0.17 +chr1 5729971 5730118 147 74 3 137.07 7242.01 0.00 +chr1 5735097 5735209 112 57 2 100.24 4828.01 0.17 +chr1 5738165 5738277 112 57 2 100.24 4828.01 0.17 +chr1 5741886 5742013 127 64 3 137.07 7242.01 0.00 +chr1 5742222 5742493 271 85 4 133.92 7242.01 0.00 +chr1 5742624 5742892 268 57 3 98.02 4828.01 0.16 +chr1 5743479 5743591 112 57 2 100.24 4828.01 0.17 +chr1 5743802 5743943 141 71 3 137.07 7242.01 0.00 +chr1 5744327 5745001 674 99 6 185.01 4828.01 0.00 +chr1 5745544 5746174 630 291 7 221.59 4828.01 0.00 +chr1 5746482 5747182 700 89 7 218.38 9656.01 0.00 +chr1 5747751 5747863 112 57 2 100.24 4828.01 0.17 +chr1 5749480 5749592 112 57 2 100.24 4828.01 0.17 diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.main --- a/tool_conf.xml.main Fri Feb 05 15:51:01 2010 -0500 +++ b/tool_conf.xml.main Fri Feb 05 16:06:27 2010 -0500 @@ -298,5 +298,9 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> - + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> </toolbox> diff -r 49961332adb6 -r e9de35947c06 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Feb 05 15:51:01 2010 -0500 +++ b/tool_conf.xml.sample Fri Feb 05 16:06:27 2010 -0500 @@ -129,8 +129,6 @@ <tool file="visualization/GMAJ.xml" /> <tool file="visualization/LAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> - <tool file="visualization/genetrack_indexer.xml" /> - <tool file="visualization/genetrack_peak_prediction.xml" /> </section> <section name="Regional Variation" id="regVar"> <tool file="regVariation/windowSplitter.xml" /> @@ -207,6 +205,11 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> <section name="Rg Data" id="rgData1"> <tool file="rgenetics/rgenetics_import.xml"/> <tool file="rgenetics/rgLpedPbed.xml"/> diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_indexer.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. + +usage: %prog input output shift +""" + +import sys, shutil, os +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import tabs2genetrack +from genetrack import logger + +if __name__ == "__main__": + import os + os.environ[ 'LC_ALL' ] = 'C' + #os.system( 'export' ) + + parser = tabs2genetrack.option_parser() + + options, args = parser.parse_args() + + # uppercase the format + options.format = options.format.upper() + + if options.format not in ('BED', 'GFF'): + sys.stdout = sys.stderr + parser.print_help() + sys.exit(-1) + + logger.disable(options.verbosity) + + # missing file names + if not (options.inpname and options.outname and options.format): + parser.print_help() + sys.exit(-1) + else: + tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ + format=options.format, shift=options.shift, index=options.index, options=options) diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_indexer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_indexer.xml Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,54 @@ +<tool id="bed2genetrack" name="GeneTrack indexer"> + + <description>on a BED file</description> + + <command interpreter="python"> + genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x + </command> + + <inputs> + + <param format="bed" name="input" type="data" help="Input data"> + <label>Select input bed file</label> + </param> + + <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> + <label>Shift at 5' end</label> + </param> + +  + + </inputs> + + <outputs> + <data format="genetrack" name="output" /> + </outputs> + +<help> +**Help** + +This tool will create a visualization of the bed file that is selected. + +**Parameters** + +- **Shift at 5' end** should be used when the location of interest is at a fixed distance from + the 5' end for **all sequenced fragments**! + + For example if the sequenced sample consists + mono-nucleosomal DNA (146bp) we should expect that + each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. + Therefore we would enter 73 as the shift parameter. Once corrected the reads + on each strand will coincide and indicate the actual midpoints + of the nucleosomes. + + When shifting the averaging process in GeneTrack is able correct for longer or shorter + than expected fragment sizes as long as the errors are reasonably random. + +</help> + +</tool> diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_peak_prediction.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,40 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. + +usage: %prog input output level sigma mode exclusion strand +""" + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import peakpred +from genetrack import logger + +if __name__ == "__main__": + + parser = peakpred.option_parser() + + options, args = parser.parse_args() + + logger.disable(options.verbosity) + + from genetrack import conf + + # trigger test mode + if options.test: + options.inpname = conf.testdata('test-hdflib-input.gtrack') + options.outname = conf.testdata('predictions.bed') + + # missing input file name + if not options.inpname and not options.outname: + parser.print_help() + else: + print 'Sigma = %s' % options.sigma + print 'Minimum peak = %s' % options.level + print 'Peak-to-peak = %s' % options.exclude + + peakpred.predict(options.inpname, options.outname, options) diff -r 49961332adb6 -r e9de35947c06 tools/genetrack/genetrack_peak_prediction.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/genetrack/genetrack_peak_prediction.xml Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,59 @@ +<tool id="predict2genetrack" name="Peak predictor"> + + <description>on GeneTrack index</description> + + <command interpreter="python"> + genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x + </command> + + <inputs> + + <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> + + <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> + <option value="gauss">Gaussian kernel</option> +  + </param> + + <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> + + + <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> + <option value="nolap">Maximal non-overlapping</option> +  + <option value="all">All peaks</option> + </param> + + <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> + </param> + + <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> + + <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> + <option value="all">Merge strands</option> +  + <option value="two">Separate strands</option> + </param> + + </inputs> + + <outputs> + <data format="bed" name="output" /> + </outputs> + +<help> +**Help** + +This tool will generate genome wide peak prediction from an index file. + +**Parameters** + +- **Smoothing method** the function used to average nearby values + +- **Smoothing value** the factor used in the method + +- **Prediction method** the function used to average nearby values + +</help> + +</tool> diff -r 49961332adb6 -r e9de35947c06 tools/peak_calling/macs_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/peak_calling/macs_wrapper.py Fri Feb 05 16:06:27 2010 -0500 @@ -0,0 +1,138 @@ +import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip +from galaxy import eggs +import pkg_resources +pkg_resources.require( "simplejson" ) +import simplejson + +CHUNK_SIZE = 1024 +ERROR_LINES = [ 'ERROR', 'command not found' ] #'Fatal' errors that should be passed back to stderr +WARNING_LINE_START = 'WARNING @' + +def gunzip_cat_glob_path( glob_path, target_filename, delete = False ): + out = open( target_filename, 'wb' ) + for filename in glob.glob( glob_path ): + fh = gzip.open( filename, 'rb' ) + while True: + data = fh.read( CHUNK_SIZE ) + if data: + out.write( data ) + else: + break + fh.close() + if delete: + os.unlink( filename ) + out.close() + +def xls_to_interval( xls_file, interval_file, header = None ): + out = open( interval_file, 'wb' ) + if header: + out.write( '#%s\n' % header ) + wrote_header = False + #From macs readme: Coordinates in XLS is 1-based which is different with BED format. + for line in open( xls_file ): + #keep all existing comment lines + if line.startswith( '#' ): + out.write( line ) + elif not wrote_header: + out.write( '#%s' % line ) + wrote_header = True + else: + fields = line.split( '\t' ) + if len( fields ) > 1: + fields[1] = str( int( fields[1] ) - 1 ) + out.write( '\t'.join( fields ) ) + out.close() + +def main(): + options = simplejson.load( open( sys.argv[1] ) ) + output_bed = sys.argv[2] + output_extra_html = sys.argv[3] + output_extra_path = sys.argv[4] + + experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for filenames (gzip of wig files will fail with spaces - macs doesn't properly escape them)..need to replace all whitespace, split makes this easier + cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) + if options['input_control']: + cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) + if 'wig' in options: + wigextend = int( options['wig']['wigextend'] ) + if wigextend >= 0: + wigextend = "--wigextend='%s'" % wigextend + else: + wigextend = '' + cmdline = "%s --wig %s --space='%s'" % ( cmdline, wigextend, options['wig']['space'] ) + if 'nomodel' in options: + cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] ) + if 'diag' in options: + cmdline = "%s --diag --fe-min='%s' --fe-max='%s' --fe-step='%s'" % ( cmdline, options['diag']['fe-min'], options['diag']['fe-max'], options['diag']['fe-step'] ) + + tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user + stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report + proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) + proc.wait() + + #Need to lightly parse stderr file to see if there is a fatal error (e.g. macs is not installed on system) + #We don't want to set tool run to error state if only warnings or info, e.g. mfold needs to be decreased, rather create empty outputs, but let user view macs log + for line in open( stderr_name ): + for err_text in ERROR_LINES: + if err_text in line: + #print error, but don't quit, allow cleanup to occur at end + print >> sys.stderr, line.rstrip( '\n\r' ) + if line.startswith( WARNING_LINE_START ): + #print warnings so they are viewable from info + print line.split( ':' )[-1].strip() + + #run R to create pdf from model script + if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ): + cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name ) + proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir ) + proc.wait() + + + #move bed out to proper output file + created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name ) + if os.path.exists( created_bed_name ): + shutil.move( created_bed_name, output_bed ) + + #parse xls files to interval files as needed + if options['xls_to_interval']: + create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) + create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name ) + if os.path.exists( create_peak_xls_file ): + xls_to_interval( create_peak_xls_file, options['xls_to_interval']['negative_peaks_file'], header = 'negative peaks file' ) + + #merge and move wig files as needed, delete gz'd files and remove emptied dirs + if 'wig' in options: + wig_base_dir = os.path.join( tmp_dir, "%s_MACS_wiggle" % experiment_name ) + if os.path.exists( wig_base_dir ): + #treatment + treatment_dir = os.path.join( wig_base_dir, "treat" ) + if os.path.exists( treatment_dir ):

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