- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2700: Forms:
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c40962280e72 changeset: 2700:c40962280e72 user: rc date: Wed Sep 16 12:39:57 2009 -0400 description: Forms: - Added 'type' and 'layout' columns to the form_definition table - Added types to forms; Request, Sample & Library info template - Added layouts to sample form definition to support multiple grids while rendering Requests: - Added 'folder_id' column to the request table - Added the Data Library Folder selectbox when creating a new request - Moved the 4 request_type methods to requests_admin from admin controller Updated the functional tests 21 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0019_request_library_folder.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/form_builder.py templates/admin/forms/edit_form.mako templates/admin/forms/manage_forms.mako templates/admin/index.mako templates/admin/requests/add_states.mako templates/admin/requests/create_request_type.mako templates/admin/requests/manage_request_types.mako templates/admin/requests/show_request.mako templates/admin/requests/view_request_type.mako templates/requests/new_request.mako templates/requests/show_request.mako test/base/twilltestcase.py test/functional/test_forms_and_requests.py diffs (1969 lines): diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/model/__init__.py Wed Sep 16 12:39:57 2009 -0400 @@ -1005,11 +1005,31 @@ return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) class FormDefinition( object ): - def __init__(self, name=None, desc=None, fields=[], current_form=None): + types = Bunch( REQUEST = 'Sequencing Request Form', + SAMPLE = 'Sequencing Sample Form', + LIBRARY_INFO_TEMPLATE = 'Library information template' ) + def __init__(self, name=None, desc=None, fields=[], current_form=None, form_type=None, layout=None): self.name = name self.desc = desc self.fields = fields self.form_definition_current = current_form + self.type = form_type + self.layout = layout + def fields_of_grid(self, layout_grid_name): + fields_dict = {} + if not layout_grid_name: + for i, f in enumerate(self.fields): + fields_dict[i] = f + else: + layout_index = -1 + for index, lg_name in enumerate(self.layout): + if lg_name == layout_grid_name: + layout_index = index + break + for i, f in enumerate(self.fields): + if f['layout'] == str(layout_index): + fields_dict[i] = f + return fields_dict class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): @@ -1025,13 +1045,14 @@ SUBMITTED = 'Submitted', COMPLETE = 'Complete') def __init__(self, name=None, desc=None, request_type=None, user=None, - form_values=None, library=None, state=False): + form_values=None, library=None, folder=None, state=False): self.name = name self.desc = desc self.type = request_type self.values = form_values self.user = user self.library = library + self.folder = folder self.state = state self.samples_list = [] def add_sample(self, sample_name=None, sample_desc=None, sample_values=None): diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/model/mapping.py Wed Sep 16 12:39:57 2009 -0400 @@ -465,7 +465,9 @@ Integer, ForeignKey( "form_definition_current.id", name='for_def_form_def_current_id_fk', use_alter=True ), index=True ), - Column( "fields", JSONType() ) ) + Column( "fields", JSONType() ), + Column( "type", TrimmedString( 255 ), index=True ), + Column( "layout", JSONType() ), ) RequestType.table = Table('request_type', metadata, Column( "id", Integer, primary_key=True), @@ -494,6 +496,7 @@ Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), + Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), Column( "state", TrimmedString( 255 ), index=True ), Column( "deleted", Boolean, index=True, default=False ) ) @@ -612,8 +615,10 @@ backref="requests" ), samples=relation( Sample, primaryjoin=( Request.table.c.id == Sample.table.c.request_id ) ), + folder=relation( LibraryFolder, + primaryjoin=( Request.table.c.folder_id == LibraryFolder.table.c.id ) ), library=relation( Library, - primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ), + primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ) ) ) assign_mapper( context, RequestType, RequestType.table, diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/model/migrate/versions/0019_request_library_folder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Wed Sep 16 12:39:57 2009 -0400 @@ -0,0 +1,84 @@ +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * +import datetime +now = datetime.datetime.utcnow +import sys, logging +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) + +def display_migration_details(): + print "========================================" + print """This script creates a request.folder_id column which is a foreign +key to the library_folder table. This also adds a 'type' and 'layout' column +to the form_definition table.""" + print "========================================" + +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + # Create the folder_id column + try: + Request_table = Table( "request", metadata, autoload=True ) + except NoSuchTableError: + Request_table = None + log.debug( "Failed loading table request" ) + if Request_table: + try: + col = Column( "folder_id", Integer, index=True ) + col.create( Request_table ) + assert col is Request_table.c.folder_id + except Exception, e: + log.debug( "Adding column 'folder_id' to request table failed: %s" % ( str( e ) ) ) + try: + LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) + except NoSuchTableError: + Request_table = None + log.debug( "Failed loading table library_folder" ) + # Add 1 foreign key constraint to the library_folder table + if Request_table and LibraryFolder_table: + try: + cons = ForeignKeyConstraint( [Request_table.c.folder_id], + [LibraryFolder_table.c.id], + name='request_folder_id_fk' ) + # Create the constraint + cons.create() + except Exception, e: + log.debug( "Adding foreign key constraint 'request_folder_id_fk' to table 'library_folder' failed: %s" % ( str( e ) ) ) + # Create the type column in form_definition + try: + FormDefinition_table = Table( "form_definition", metadata, autoload=True ) + except NoSuchTableError: + FormDefinition_table = None + log.debug( "Failed loading table form_definition" ) + if FormDefinition_table: + try: + col = Column( "type", TrimmedString( 255 ), index=True ) + col.create( FormDefinition_table ) + assert col is FormDefinition_table.c.type + except Exception, e: + log.debug( "Adding column 'type' to form_definition table failed: %s" % ( str( e ) ) ) + try: + col = Column( "layout", JSONType()) + col.create( FormDefinition_table ) + assert col is FormDefinition_table.c.layout + except Exception, e: + log.debug( "Adding column 'layout' to form_definition table failed: %s" % ( str( e ) ) ) + + +def downgrade(): + pass diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Wed Sep 16 12:39:57 2009 -0400 @@ -749,122 +749,3 @@ else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype ) - @web.expose - @web.require_admin - def manage_request_types( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) - forms = get_all_forms(trans, all_versions=True) - request_types_list = trans.app.model.RequestType.query().all() - if show_filter == 'All': - request_types = request_types_list - elif show_filter == 'Deleted': - request_types = [rt for rt in request_types_list if rt.deleted] - else: - request_types = [rt for rt in request_types_list if not rt.deleted] - return trans.fill_template( '/admin/requests/manage_request_types.mako', - request_types=request_types, - forms=forms, - show_filter=show_filter, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def request_type( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'create', False ): - return trans.fill_template( '/admin/requests/create_request_type.mako', - forms=get_all_forms( trans, - filter=dict(deleted=False) ), - msg=msg, - messagetype=messagetype) - elif params.get( 'define_states_button', False ): - return trans.fill_template( '/admin/requests/add_states.mako', - request_type_name=util.restore_text( params.name ), - desc=util.restore_text( params.description ), - num_states=int(util.restore_text( params.num_states )), - request_form_id=int(util.restore_text( params.request_form_id )), - sample_form_id=int(util.restore_text( params.sample_form_id )), - msg=msg, - messagetype=messagetype) - elif params.get( 'save_request_type', False ): - st, msg = self._save_request_type(trans, **kwd) - if not st: - return trans.fill_template( '/admin/requests/create_request_type.mako', - forms=get_all_forms( trans ), - msg=msg, - messagetype='error') - return trans.response.send_redirect( web.url_for( controller='admin', - action='manage_request_types', - msg='Request type <b>%s</b> has been created' % st.name, - messagetype='done') ) - elif params.get('view', False): - rt = trans.app.model.RequestType.get(int(util.restore_text( params.id ))) - ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() - return trans.fill_template( '/admin/requests/view_request_type.mako', - request_type=rt, - forms=get_all_forms( trans ), - states_list=ss_list, - deleted=False, - show_deleted=False, - msg=msg, - messagetype=messagetype ) - def _save_request_type(self, trans, **kwd): - params = util.Params( kwd ) - num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) - proceed = True - for i in range( num_states ): - if not util.restore_text( params.get( 'state_name_%i' % i, None ) ): - proceed = False - break - if not proceed: - msg = "All the state name(s) must be completed." - return None, msg - rt = trans.app.model.RequestType() - rt.name = util.restore_text( params.name ) - rt.desc = util.restore_text( params.description ) or "" - rt.request_form = trans.app.model.FormDefinition.get(int( params.request_form_id )) - rt.sample_form = trans.app.model.FormDefinition.get(int( params.sample_form_id )) - rt.flush() - # set sample states - ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() - for ss in ss_list: - ss.delete() - ss.flush() - for i in range( num_states ): - name = util.restore_text( params.get( 'state_name_%i' % i, None )) - desc = util.restore_text( params.get( 'state_desc_%i' % i, None )) - ss = trans.app.model.SampleState(name, desc, rt) - ss.flush() - msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) - return rt, msg - @web.expose - @web.require_admin - def delete_request_type( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id ))) - rt.deleted = True - rt.flush() - return trans.response.send_redirect( web.url_for( controller='admin', - action='manage_request_types', - msg='Request type <b>%s</b> has been deleted' % rt.name, - messagetype='done') ) - @web.expose - @web.require_admin - def undelete_request_type( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id ))) - rt.deleted = False - rt.flush() - return trans.response.send_redirect( web.url_for( controller='admin', - action='manage_request_types', - msg='Request type <b>%s</b> has been undeleted' % rt.name, - messagetype='done') ) diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Wed Sep 16 12:39:57 2009 -0400 @@ -31,37 +31,72 @@ show_filter = params.get( 'show_filter', 'Active' ) return self._show_forms_list(trans, msg, messagetype, show_filter) def _show_forms_list(self, trans, msg, messagetype, show_filter='Active'): - fdc_list = trans.app.model.FormDefinitionCurrent.query().all() + all_forms = trans.app.model.FormDefinitionCurrent.query().all() if show_filter == 'All': - forms_list = fdc_list + forms_list = all_forms elif show_filter == 'Deleted': - forms_list = [form for form in fdc_list if form.deleted] + forms_list = [form for form in all_forms if form.deleted] else: - forms_list = [form for form in fdc_list if not form.deleted] + forms_list = [form for form in all_forms if not form.deleted] return trans.fill_template( '/admin/forms/manage_forms.mako', fdc_list=forms_list, + all_forms=all_forms, show_filter=show_filter, msg=msg, messagetype=messagetype ) + def __form_types_widget(self, trans, selected='none'): + form_type_selectbox = SelectField( 'form_type_selectbox', + refresh_on_change=True, + refresh_on_change_values=[trans.app.model.FormDefinition.types.SAMPLE] ) + if selected == 'none': + form_type_selectbox.add_option('Select one', 'none', selected=True) + else: + form_type_selectbox.add_option('Select one', 'none') + for ft in trans.app.model.FormDefinition.types.items(): + if selected == ft[1]: + form_type_selectbox.add_option(ft[1], ft[1], selected=True) + else: + form_type_selectbox.add_option(ft[1], ft[1]) + return form_type_selectbox + @web.expose @web.require_admin def new( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) + self.__imported_from_file = False if params.get( 'create_form_button', False ): fd, msg = self.__save_form( trans, fdc_id=None, **kwd ) + if not fd: + return trans.response.send_redirect( web.url_for( controller='forms', + action='new', + msg=msg, + messagetype='error' ) ) self.__get_saved_form( fd ) - return trans.response.send_redirect( web.url_for( controller='forms', - action='edit', - form_id=fd.id, - show_form=True ) ) + if self.__imported_from_file: + return trans.response.send_redirect( web.url_for( controller='forms', + action='edit', + show_form=True, + form_id=fd.id) ) + else: + return trans.response.send_redirect( web.url_for( controller='forms', + action='edit', + form_id=fd.id, + add_field_button='Add field', + num_fields=0, + name=fd.name, + description=fd.desc, + form_type_selectbox=fd.type ) ) self.current_form = {} self.current_form[ 'name' ] = 'New Form' self.current_form[ 'desc' ] = '' + self.current_form['type'] = 'none' + self.current_form[ 'layout' ] = ['Main'] self.current_form[ 'fields' ] = [] inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), + ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ), ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', inputs=inputs, @@ -115,12 +150,19 @@ # The following two dicts store the unsaved select box options self.del_options = {} self.add_options = {} - if fd.fields: - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) - else: - # If the form is empty, we'll simulate a click on the add_field_button so the - # form will be displayed with the field choice, saving a mouse click. - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, empty_form=True, **kwd ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + #Add a layout grid + elif params.get( 'add_layout_grid', False ): + self.__update_current_form( trans, **kwd ) + self.__add_layout_grid() + # show the form again + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + # Delete a layout grid + elif params.get( 'remove_layout_grid_button', False ): + self.__update_current_form( trans, **kwd ) + index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1 + self.__remove_layout_grid( index ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) # Delete a field elif params.get( 'remove_button', False ): self.__update_current_form( trans, **kwd ) @@ -163,7 +205,11 @@ elif params.get( 'select_box_options', False ) == 'add': index = int( kwd[ 'field_index' ] ) self.current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) - return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + def __add_layout_grid(self): + self.current_form['layout'].append('') + def __remove_layout_grid(self, index): + del self.current_form['layout'][index] def __remove_field(self, index): del self.current_form['fields'][index] def __add_field(self): @@ -175,7 +221,8 @@ 'visible': True, 'required': False, 'type': BaseField.form_field_types()[0], - 'selectlist': [] } + 'selectlist': [], + 'layout': 'none' } self.current_form['fields'].append(empty_field) def __get_field(self, index, **kwd): params = util.Params( kwd ) @@ -187,6 +234,7 @@ helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) ) required = params.get( 'field_required_%i' % index, False ) field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) ) + layout = params.get( 'field_layout_%i' % index, '' ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(index, **kwd) return {'label': name, @@ -194,12 +242,14 @@ 'visible': True, 'required': required, 'type': field_type, - 'selectlist': selectlist } + 'selectlist': selectlist, + 'layout': layout } return {'label': name, 'helptext': helptext, 'visible': True, 'required': required, - 'type': field_type} + 'type': field_type, + 'layout': layout} def __get_selectbox_options(self, index, **kwd): ''' This method gets all the options entered by the user for field when @@ -219,6 +269,8 @@ self.current_form = {} self.current_form['name'] = fd.name self.current_form['desc'] = fd.desc + self.current_form['type'] = fd.type + self.current_form['layout'] = list(copy.deepcopy(fd.layout)) self.current_form['fields'] = list(copy.deepcopy(fd.fields)) def __validate_form(self, **kwd): ''' @@ -230,6 +282,9 @@ # form name if not util.restore_text( params.name ): return None, 'Form name must be filled.' + # form type + if util.restore_text( params.form_type_selectbox ) == 'none': + return None, 'Form type must be selected.' # fields for i in range( len(self.current_form['fields']) ): if not util.restore_text(params.get( 'field_name_%i' % i, None )): @@ -239,6 +294,11 @@ params = util.Params( kwd ) name = util.restore_text( params.name ) desc = util.restore_text( params.description ) or "" + form_type = util.restore_text( params.form_type_selectbox ) + layout = [] + if form_type == trans.app.model.FormDefinition.types.SAMPLE: + for index in range(len(self.current_form[ 'layout' ])): + layout.append(params.get( 'grid_layout%i' % index, '' )) csv_file = params.get( 'file_data', '' ) if csv_file == '': # set form fields @@ -247,16 +307,18 @@ fields.append(self.__get_field(i, **kwd)) fields = fields else: - fields = self.__import_fields(trans, csv_file) - return name, desc, fields + fields = self.__import_fields(trans, csv_file, form_type) + return name, desc, form_type, layout, fields def __update_current_form(self, trans, **kwd): - name, desc, fields = self.__get_form(trans, **kwd) + name, desc, form_type, layout, fields = self.__get_form(trans, **kwd) self.current_form = {} self.current_form['name'] = name self.current_form['desc'] = desc + self.current_form['type'] = form_type + self.current_form['layout'] = layout self.current_form['fields'] = fields - def __import_fields(self, trans, csv_file): + def __import_fields(self, trans, csv_file, form_type): ''' "company","name of the company", "True", "required", "TextField",, "due date","turnaround time", "True", "optional", "SelectField","24 hours, 1 week, 1 month" @@ -265,20 +327,32 @@ fields = [] try: reader = csv.reader(csv_file.file) - for row in reader: - options = row[5].split(',') - fields.append({'label': row[0], - 'helptext': row[1], - 'visible': row[2], - 'required': row[3], - 'type': row[4], - 'selectlist': options}) + if form_type == trans.app.model.FormDefinition.types.SAMPLE: + for row in reader: + options = row[5].split(',') + fields.append({'label': row[0], + 'helptext': row[1], + 'visible': row[2], + 'required': row[3], + 'type': row[4], + 'selectlist': options, + 'layout':row[6]}) + else: + for row in reader: + options = row[5].split(',') + fields.append({'label': row[0], + 'helptext': row[1], + 'visible': row[2], + 'required': row[3], + 'type': row[4], + 'selectlist': options}) except: return trans.response.send_redirect( web.url_for( controller='forms', action='new', status='error', message='Error in importing <b>%s</b> file' % csv_file, **kwd)) + self.__imported_from_file = True return fields def __save_form(self, trans, fdc_id=None, **kwd): @@ -290,7 +364,7 @@ if not flag: return None, msg fd = trans.app.model.FormDefinition() - fd.name, fd.desc, fd.fields = self.__get_form(trans, **kwd) + fd.name, fd.desc, fd.type, fd.layout, fd.fields = self.__get_form(trans, **kwd) if fdc_id: # save changes to the existing form # change the pointer in the form_definition_current table to point # to this new record @@ -306,7 +380,7 @@ return fd, msg class FieldUI(object): - def __init__(self, index, field=None, field_type=None): + def __init__(self, layout_grids, index, field=None, field_type=None): ''' This method returns a list of widgets which describes a field. This includes label, helptext, type, & required/optional @@ -323,6 +397,11 @@ self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) + self.layout_grids = layout_grids + if layout_grids: + self.layout_selectbox = SelectField('field_layout_'+str(index)) + for index, grid_name in enumerate(layout_grids): + self.layout_selectbox.add_option("%i. %s" %(index+1, grid_name), index) if field: self.fill(field, field_type) def fill(self, field, field_type=None): @@ -350,6 +429,14 @@ self.required = SelectField('field_required_'+str(self.index), display='radio') self.required.add_option('Required', 'required', selected=True) self.required.add_option('Optional', 'optional') + # layout + if self.layout_grids: + self.layout_selectbox = SelectField('field_layout_'+str(self.index)) + for i, grid_name in enumerate(self.layout_grids): + if field['layout'] == str(i): + self.layout_selectbox.add_option("%i. %s" %(i+1, grid_name), i, selected=True) + else: + self.layout_selectbox.add_option("%i. %s" %(i+1, grid_name), i) def selectbox_ui(self, field): self.selectbox_options = [] if field['selectlist']: @@ -358,6 +445,12 @@ TextField('field_'+str(self.index)+'_option_'+str(ctr), 40, option))) def get(self): + if self.layout_grids: + return [( 'Label', self.label ), + ( 'Help text', self.helptext ), + ( 'Type', self.fieldtype, self.selectbox_options), + ( '', self.required), + ( 'Select the grid layout to place this field', self.layout_selectbox)] return [( 'Label', self.label ), ( 'Help text', self.helptext ), ( 'Type', self.fieldtype, self.selectbox_options), @@ -367,31 +460,29 @@ def label(self): return str(self.index)+'.'+self.label - def __show( self, trans, form, msg='', messagetype='done', empty_form=False, **kwd ): + def __show( self, trans, form, msg='', messagetype='done', **kwd ): ''' This method displays the form and any of the changes made to it, The empty_form param allows for this method to simulate clicking the "add_field_button" on the edit_form.mako page so that the page is displayed with the first field to be added, saving a mouse click. ''' - if empty_form: - # Send params that will simulate a button click on the add_field_button - # button on edit_form.mako. - param_dict = { 'form_id' : str( form.id ), - 'num_fields' : '0', - 'refresh' : 'true', - 'name' : form.name, - 'description' : form.desc, - 'add_field_button' : 'Add field' } - self.edit( trans, **param_dict ) params = util.Params( kwd ) # name & description form_details = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), - ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ) ] + ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), + ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ) ] + form_layout = [] + if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE: + for index, lg in enumerate(self.current_form['layout']): + form_layout.append( TextField( 'grid_layout%i' % index, 40, lg )) # fields field_details = [] for index, field in enumerate( self.current_form[ 'fields' ] ): - field_ui = self.FieldUI( index, field ) + if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE: + field_ui = self.FieldUI( self.current_form['layout'], index, field ) + else: + field_ui = self.FieldUI( None, index, field ) field_details.append( field_ui.get() ) return trans.fill_template( '/admin/forms/edit_form.mako', form_details=form_details, @@ -399,10 +490,12 @@ form=form, field_types=BaseField.form_field_types(), msg=msg, - messagetype=messagetype ) + messagetype=messagetype, + current_form_type=self.current_form['type'], + layout_grids=form_layout ) # Common methods for all components that use forms -def get_all_forms( trans, all_versions=False, filter=None ): +def get_all_forms( trans, all_versions=False, filter=None, form_type='All' ): ''' Return all the latest forms from the form_definition_current table if all_versions is set to True. Otherwise return all the versions @@ -418,7 +511,11 @@ fdc_list = trans.app.model.FormDefinitionCurrent.query().filter_by(**filter) else: fdc_list = trans.app.model.FormDefinitionCurrent.query().all() - return [ fdc.latest_form for fdc in fdc_list ] + if form_type == 'All': + return [ fdc.latest_form for fdc in fdc_list ] + else: + return [ fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type ] + def get_form_widgets( trans, form, contents=[], user=None, **kwd ): diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Wed Sep 16 12:39:57 2009 -0400 @@ -1100,7 +1100,8 @@ library_id=library_id, folder_id=folder_id, ldda_id=ldda_id, - forms=get_all_forms( trans, filter=dict(deleted=False) ), + forms=get_all_forms( trans, filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ), msg=msg, messagetype=messagetype ) @web.expose diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Wed Sep 16 12:39:57 2009 -0400 @@ -148,7 +148,7 @@ request_details.append(dict(label='Date created', value=request.create_time, helptext='')) - # library associated + # library associated if request.library: value = request.library.name else: @@ -156,6 +156,14 @@ request_details.append( dict( label='Data library', value=value, helptext='Data library where the resultant dataset will be stored' ) ) + # folder associated + if request.folder: + value = request.folder.name + else: + value = None + request_details.append( dict( label='Data library folder', + value=value, + helptext='Data library folder where the resultant dataset will be stored' ) ) # form fields for index, field in enumerate(request.type.request_form.fields): if field['required']: @@ -230,7 +238,7 @@ return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message='Error in importing <b>%s</b> samples file' % file_obj.file, + message='Error in importing samples file', **kwd)) elif params.get('add_sample_button', False) == 'Add New': # save the all (saved+unsaved) sample info in 'current_samples' @@ -488,7 +496,9 @@ def __library_ui(self, libraries, request=None, **kwd): params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=['new'] ) + lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()] + lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list ) + folders = [] if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) @@ -499,23 +509,48 @@ for lib, hidden_folder_ids in libraries.items(): if str(lib.id) == lib_id: lib_list.add_option(lib.name, lib.id, selected=True) + folders.append( lib.root_folder ) + for f in lib.root_folder.folders: + if str(f.id) not in hidden_folder_ids.split(','): + folders.append( f ) else: lib_list.add_option(lib.name, lib.id) + lib_list.refresh_on_change_values.append(lib.id) if lib_id == 'new': lib_list.add_option('Create a new data library', 'new', selected=True) else: lib_list.add_option('Create a new data library', 'new') - widget = dict(label='Data library', - widget=lib_list, - helptext='Data library where the resultant dataset will be stored.') + lib_widget = dict(label='Data library', + widget=lib_list, + helptext='Data library where the resultant dataset will be stored.') + if folders: + if request: + if request.folder: + current_fid = request.folder.id + else: + current_fid = request.library.root_folder.id + else: + current_fid = params.get( 'folder_id', 'none' ) + folder_list = SelectField( 'folder_id') + for f in folders: + if str(f.id) == current_fid: + folder_list.add_option(f.name, f.id, selected=True) + else: + folder_list.add_option(f.name, f.id) + folder_widget = dict(label='Folder', + widget=folder_list, + helptext='Folder of the selected data library where the resultant dataset will be stored.') if lib_id == 'new': new_lib = dict(label='Create a new data library', widget=TextField('new_library_name', 40, util.restore_text( params.get( 'new_library_name', '' ) )), helptext='Enter a name here to request a new data library') - return [widget, new_lib] + return [lib_widget, new_lib] else: - return [widget] + if folders: + return [lib_widget, folder_widget] + else: + return [lib_widget] def __validate(self, trans, request): ''' Validates the request entered by the user @@ -546,6 +581,13 @@ library = trans.app.model.Library.get(int(params.get('library_id', None))) except: library = None + try: + folder = trans.app.model.LibraryFolder.get(int(params.get('folder_id', None))) + except: + if library: + folder = library.root_folder + else: + folder = None # fields values = [] for index, field in enumerate(request_type.request_form.fields): @@ -577,7 +619,7 @@ if not request: request = trans.app.model.Request(name, desc, request_type, trans.user, form_values, - library=library, + library=library, folder=folder, state=trans.app.model.Request.states.UNSUBMITTED) request.flush() else: @@ -587,6 +629,7 @@ request.user = trans.user request.values = form_values request.library = library + request.folder = folder request.state = trans.app.model.Request.states.UNSUBMITTED request.flush() return request diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Sep 16 12:39:57 2009 -0400 @@ -8,6 +8,7 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from galaxy.web.controllers.forms import get_form_widgets +from galaxy.web.controllers.forms import get_all_forms log = logging.getLogger( __name__ ) @@ -100,6 +101,7 @@ else: self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) + self.__update_request_state(trans) # Render the list view return self.request_grid( trans, **kwargs ) @web.expose @@ -553,8 +555,17 @@ else: value = None request_details.append(dict(label='Data library', - value=value, - helptext='Data library where the resultant dataset will be stored')) + value=value, + helptext='Data library where the resultant dataset will be stored')) + # folder associated + if request.folder: + value = request.folder.name + else: + value = None + request_details.append( dict( label='Data library folder', + value=value, + helptext='Data library folder where the resultant dataset will be stored' ) ) + # form fields for index, field in enumerate(request.type.request_form.fields): if field['required']: @@ -714,26 +725,31 @@ """ params = util.Params( kwd ) lib_id = params.get( 'library_id', 'none' ) - all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ - .order_by( trans.app.model.Library.name ).all() - roles = user.all_roles() - actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] - # The libraries dictionary looks like: { library : '1,2' }, library : '3' } - # Its keys are the libraries that should be displayed for the current user and whose values are a - # string of comma-separated folder ids, of the associated folders the should NOT be displayed. - # The folders that should not be displayed may not be a complete list, but it is ultimately passed - # to the calling method to keep from re-checking the same folders when the library / folder - # select lists are rendered. - # - # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids - # so that you do not need to check those same folders yet again when populating the select list. - # - libraries = {} - for library in all_libraries: - can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) - if can_show: - libraries[ library ] = hidden_folder_ids - lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=['new'] ) + if not user: + libraries = {} + else: + all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ).all() + roles = user.all_roles() + actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] + # The libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + # + # TODO: RC, when you add the folders select list to your request form, take advantage of the hidden_folder_ids + # so that you do not need to check those same folders yet again when populating the select list. + # + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids + lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()] + lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list ) + folders = [] if request and lib_id == 'none': if request.library: lib_id = str(request.library.id) @@ -744,23 +760,48 @@ for lib, hidden_folder_ids in libraries.items(): if str(lib.id) == lib_id: lib_list.add_option(lib.name, lib.id, selected=True) + folders.append( lib.root_folder ) + for f in lib.root_folder.folders: + if str(f.id) not in hidden_folder_ids.split(','): + folders.append( f ) else: lib_list.add_option(lib.name, lib.id) + lib_list.refresh_on_change_values.append(lib.id) if lib_id == 'new': lib_list.add_option('Create a new data library', 'new', selected=True) else: lib_list.add_option('Create a new data library', 'new') - widget = dict(label='Data library', - widget=lib_list, - helptext='Data library where the resultant dataset will be stored.') + lib_widget = dict(label='Data library', + widget=lib_list, + helptext='Data library where the resultant dataset will be stored.') + if folders: + if request: + if request.folder: + current_fid = request.folder.id + else: + current_fid = request.library.root_folder.id + else: + current_fid = params.get( 'folder_id', 'none' ) + folder_list = SelectField( 'folder_id') + for f in folders: + if str(f.id) == current_fid: + folder_list.add_option(f.name, f.id, selected=True) + else: + folder_list.add_option(f.name, f.id) + folder_widget = dict(label='Folder', + widget=folder_list, + helptext='Folder of the selected data library where the resultant dataset will be stored.') if lib_id == 'new': - new_lib = dict(label='Create a new Library', + new_lib = dict(label='Create a new data library', widget=TextField('new_library_name', 40, util.restore_text( params.get( 'new_library_name', '' ) )), - helptext='Enter a library name here to request a new library') - return [widget, new_lib] + helptext='Enter a name here to request a new data library') + return [lib_widget, new_lib] else: - return [widget] + if folders: + return [lib_widget, folder_widget] + else: + return [lib_widget] def __validate(self, trans, request): ''' Validates the request entered by the user @@ -795,6 +836,13 @@ library = trans.app.model.Library.get(int(params.get('library_id', None))) except: library = None + try: + folder = trans.app.model.LibraryFolder.get(int(params.get('folder_id', None))) + except: + if library: + folder = library.root_folder + else: + folder = None # fields values = [] for index, field in enumerate(request_type.request_form.fields): @@ -826,7 +874,7 @@ if not request: request = trans.app.model.Request(name, desc, request_type, user, form_values, - library=library, + library=library, folder=folder, state=trans.app.model.Request.states.UNSUBMITTED) request.flush() else: @@ -836,6 +884,7 @@ request.user = user request.values = form_values request.library = library + request.folder = folder request.flush() return request @web.expose @@ -934,6 +983,13 @@ request_id=request.id, msg='Bar codes has been saved for this request', messagetype='done')) + + def __update_request_state(self, trans): + requests = trans.app.model.Request.query.filter_by(deleted=False, + state=trans.app.model.Request.states.SUBMITTED) + for request in requests: + self.__set_request_state(request) + def __set_request_state(self, request): # check if all the samples of the current request are in the final state complete = True @@ -1013,4 +1069,128 @@ return trans.fill_template( '/admin/samples/events.mako', events_list=events_list, sample=sample, widgets=widgets, title=title) - \ No newline at end of file + + # Request Type Stuff + @web.expose + @web.require_admin + def manage_request_types( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) + forms = get_all_forms(trans, all_versions=True) + request_types_list = trans.app.model.RequestType.query().all() + if show_filter == 'All': + request_types = request_types_list + elif show_filter == 'Deleted': + request_types = [rt for rt in request_types_list if rt.deleted] + else: + request_types = [rt for rt in request_types_list if not rt.deleted] + return trans.fill_template( '/admin/requests/manage_request_types.mako', + request_types=request_types, + forms=forms, + show_filter=show_filter, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def request_type( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'create', False ): + return trans.fill_template( '/admin/requests/create_request_type.mako', + request_forms=get_all_forms( trans, + filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.REQUEST ), + sample_forms=get_all_forms( trans, + filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.SAMPLE ), + msg=msg, + messagetype=messagetype) + elif params.get( 'define_states_button', False ): + return trans.fill_template( '/admin/requests/add_states.mako', + request_type_name=util.restore_text( params.name ), + desc=util.restore_text( params.description ), + num_states=int(util.restore_text( params.num_states )), + request_form_id=int(util.restore_text( params.request_form_id )), + sample_form_id=int(util.restore_text( params.sample_form_id )), + msg=msg, + messagetype=messagetype) + elif params.get( 'save_request_type', False ): + st, msg = self.__save_request_type(trans, **kwd) + if not st: + return trans.fill_template( '/admin/requests/create_request_type.mako', + forms=get_all_forms( trans ), + msg=msg, + messagetype='error') + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_request_types', + msg='Request type <b>%s</b> has been created' % st.name, + messagetype='done') ) + elif params.get('view', False): + rt = trans.app.model.RequestType.get(int(util.restore_text( params.id ))) + ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() + return trans.fill_template( '/admin/requests/view_request_type.mako', + request_type=rt, + forms=get_all_forms( trans ), + states_list=ss_list, + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + def __save_request_type(self, trans, **kwd): + params = util.Params( kwd ) + num_states = int( util.restore_text( params.get( 'num_states', 0 ) )) + proceed = True + for i in range( num_states ): + if not util.restore_text( params.get( 'state_name_%i' % i, None ) ): + proceed = False + break + if not proceed: + msg = "All the state name(s) must be completed." + return None, msg + rt = trans.app.model.RequestType() + rt.name = util.restore_text( params.name ) + rt.desc = util.restore_text( params.description ) or "" + rt.request_form = trans.app.model.FormDefinition.get(int( params.request_form_id )) + rt.sample_form = trans.app.model.FormDefinition.get(int( params.sample_form_id )) + rt.flush() + # set sample states + ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() + for ss in ss_list: + ss.delete() + ss.flush() + for i in range( num_states ): + name = util.restore_text( params.get( 'state_name_%i' % i, None )) + desc = util.restore_text( params.get( 'state_desc_%i' % i, None )) + ss = trans.app.model.SampleState(name, desc, rt) + ss.flush() + msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) + return rt, msg + @web.expose + @web.require_admin + def delete_request_type( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id ))) + rt.deleted = True + rt.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_request_types', + msg='Request type <b>%s</b> has been deleted' % rt.name, + messagetype='done') ) + @web.expose + @web.require_admin + def undelete_request_type( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id ))) + rt.deleted = False + rt.flush() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_request_types', + msg='Request type <b>%s</b> has been undeleted' % rt.name, + messagetype='done') ) diff -r 1fb29bd2725a -r c40962280e72 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Wed Sep 16 11:27:50 2009 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Sep 16 12:39:57 2009 -0400 @@ -12,7 +12,7 @@ raise TypeError( "Abstract Method" ) @staticmethod def form_field_types(): - return ['TextField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField'] + return ['TextField', 'NumberField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField'] class TextField(BaseField): """ @@ -29,6 +29,25 @@ self.value = value or "" def get_html( self, prefix="" ): return '<input type="text" name="%s%s" size="%d" value="%s">' \ + % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) + def set_size(self, size): + self.size = int( size ) + +class NumberField(BaseField): + """ + A number input box. + + >>> print NumberField( "foo" ).get_html() + <input type="int" name="foo" size="10" value=""> + >>> print NumberField( "bins", size=4, value="12345" ).get_html() + <input type="int" name="bins" size="4" value="12345"> + """ + def __init__( self, name, size=None, value=None ): + self.name = name + self.size = int( size or 10 ) + self.value = value or "" + def get_html( self, prefix="" ): + return '<input type="int" name="%s%s" size="%d" value="%s">' \ % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) def set_size(self, size): self.size = int( size ) diff -r 1fb29bd2725a -r c40962280e72 templates/admin/forms/edit_form.mako --- a/templates/admin/forms/edit_form.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/forms/edit_form.mako Wed Sep 16 12:39:57 2009 -0400 @@ -69,6 +69,16 @@ </div> </%def> +<%def name="render_layout( index, widget )"> + <div class="repeat-group-item"> + <div class="form-row"> + <b> ${index+1}</b> + ${widget.get_html()} + <input type="submit" name="remove_layout_grid_button" value="Remove grid ${index+1}"/> + </div> + </div> +</%def> + <div class="toolForm"> <div class="toolFormTitle">Edit form definition "${form.name}"</div> <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" > @@ -81,6 +91,18 @@ <div style="clear: both"></div> </div> %endfor + %if current_form_type == trans.app.model.FormDefinition.types.SAMPLE: + <div class="toolFormTitle">Form Layout</div> + <div class="form-row"> + <label>Layout grid names</label> + </div> + %for index, lg in enumerate(layout_grids): + ${render_layout( index, lg )} + %endfor + <div class="form-row"> + <input type="submit" name="add_layout_grid" value="Add layout grid"/> + </div> + %endif <div class="toolFormTitle">Fields (${len(form.fields)})</div> %for ctr, field in enumerate(field_details): ${render_field( ctr, field )} diff -r 1fb29bd2725a -r c40962280e72 templates/admin/forms/manage_forms.mako --- a/templates/admin/forms/manage_forms.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/forms/manage_forms.mako Wed Sep 16 12:39:57 2009 -0400 @@ -29,6 +29,7 @@ %endif </td> <td><i>${form.desc}</i></td> + <td>${form.type}</td> </tr> </%def> @@ -41,7 +42,7 @@ </li> </ul> -%if not fdc_list: +%if not all_forms: There are no forms. %else: <div class="grid-header"> @@ -61,6 +62,7 @@ <tr> <th>Name</th> <th>Description</th> + <th>Type</th> </tr> </thead> <tbody> diff -r 1fb29bd2725a -r c40962280e72 templates/admin/index.mako --- a/templates/admin/index.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/index.mako Wed Sep 16 12:39:57 2009 -0400 @@ -118,7 +118,7 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='manage_request_types' )}" target="galaxy_main">Manage request types</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='manage_request_types' )}" target="galaxy_main">Manage request types</a></div> <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='list')}" target="galaxy_main">Manage requests</a></div> </div> </div> diff -r 1fb29bd2725a -r c40962280e72 templates/admin/requests/add_states.mako --- a/templates/admin/requests/add_states.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/requests/add_states.mako Wed Sep 16 12:39:57 2009 -0400 @@ -7,7 +7,7 @@ <div class="toolForm"> <div class="toolFormTitle">Create ${num_states} states for the '${request_type_name}' request type</div> - <form name="new_form_fields" action="${h.url_for( controller='admin', action='request_type', name=request_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" > + <form name="new_form_fields" action="${h.url_for( controller='requests_admin', action='request_type', name=request_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" > <div class="toolFormBody"> %for element_count in range( num_states ): <div class="form-row"> diff -r 1fb29bd2725a -r c40962280e72 templates/admin/requests/create_request_type.mako --- a/templates/admin/requests/create_request_type.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/requests/create_request_type.mako Wed Sep 16 12:39:57 2009 -0400 @@ -8,11 +8,11 @@ <div class="toolForm"> <div class="toolFormTitle">Create a new request type</div> - %if not forms: - Create a form definition first to create a new request type. + %if not request_forms or not sample_forms: + Create a request & sample form definition first to create a new request type. %else: <div class="toolFormBody"> - <form name="create_request_type" action="${h.url_for( controller='admin', action='request_type')}" method="post" > + <form name="create_request_type" action="${h.url_for( controller='requests_admin', action='request_type')}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> @@ -32,7 +32,7 @@ Request Form definition: </label> <select name="request_form_id"> - %for form in forms: + %for form in request_forms: <option value="${form.id}">${form.name}</option> %endfor </select> @@ -42,7 +42,7 @@ Sample Form definition: </label> <select name="sample_form_id"> - %for form in forms: + %for form in sample_forms: <option value="${form.id}">${form.name}</option> %endfor </select> diff -r 1fb29bd2725a -r c40962280e72 templates/admin/requests/manage_request_types.mako --- a/templates/admin/requests/manage_request_types.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/requests/manage_request_types.mako Wed Sep 16 12:39:57 2009 -0400 @@ -13,7 +13,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='request_type', create=True )}"><span>Create a new request type</span></a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='request_type', create=True )}"><span>Create a new request type</span></a> </li> </ul> @@ -24,9 +24,9 @@ <span>|</span> %endif %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='admin', action='manage_request_types', show_filter=filter )}"><b>${filter}</b></a></span> + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='manage_request_types', show_filter=filter )}"><b>${filter}</b></a></span> %else: - <span class="filter"><a href="${h.url_for( controller='admin', action='manage_request_types', show_filter=filter )}">${filter}</a></span> + <span class="filter"><a href="${h.url_for( controller='requests_admin', action='manage_request_types', show_filter=filter )}">${filter}</a></span> %endif %endfor </div> @@ -46,7 +46,7 @@ %for request_type in request_types: <tr> <td> - <a href="${h.url_for( controller='admin', action='request_type', view='True', id=request_type.id)}">${request_type.name}</a> + <a href="${h.url_for( controller='requests_admin', action='request_type', view='True', id=request_type.id)}">${request_type.name}</a> <a id="request_type-${request_type.id}-popup" class="popup-arrow" style="display: none;">▼</a> %if request_type.deleted: <div popupmenu="request_type-${request_type.id}-popup"> diff -r 1fb29bd2725a -r c40962280e72 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/requests/show_request.mako Wed Sep 16 12:39:57 2009 -0400 @@ -26,18 +26,39 @@ %endif </ul> -<%def name="render_sample_form( index, sample_name, sample_values )"> - <td> - <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> - <div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> - </div> - </td> - <td> - </td> - %for field_index, field in enumerate(request.type.sample_form.fields): + +<%def name="render_sample_form( index, sample_name, sample_values, grid_index, fields_dict )"> + %if grid_index == 0: <td> - <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/> + <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${' (required)' }</i> + </div> + </td> + <td> + </td> + %else: + <td> + ${sample_name} + </td> + %endif + %for field_index, field in fields_dict.items(): + <td> + %if field['type'] == 'TextField': + <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> + %elif field['type'] == 'SelectField': + <select name="sample_${index}_field_${field_index}" last_selected_value="2"> + %for option_index, option in enumerate(field['selectlist']): + %if option == sample_values[field_index]: + <option value="${option}" selected>${option}</option> + %else: + <option value="${option}">${option}</option> + %endif + %endfor + </select> + %elif field['type'] == 'CheckboxField': + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %endif <div class="toolParamHelp" style="clear: both;"> <i>${'('+field['required']+')' }</i> </div> @@ -45,18 +66,20 @@ %endfor </%def> -<%def name="render_sample( index, sample )"> +<%def name="render_sample( index, sample, grid_index, fields_dict )"> <td> ${sample.name} </td> - <td> - %if sample.request.unsubmitted(): - Unsubmitted - %else: - <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> - %endif - </td> - %for field_index, field in enumerate(request.type.sample_form.fields): + %if grid_index == 0: + <td> + %if sample.request.unsubmitted(): + Unsubmitted + %else: + <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %endif + </td> + %endif + %for field_index, field in fields_dict.items(): <td> %if sample.values.content[field_index]: ${sample.values.content[field_index]} @@ -65,7 +88,6 @@ %endif </td> %endfor - </%def> <div class="toolForm"> @@ -100,58 +122,81 @@ </div> </div> +<%def name="render_grid( grid_index, grid_name, fields_dict )"> + %if grid_name: + <div class="toolFormTitle">${grid_name}</div> + %endif + <div style="clear: both"></div> + <table class="grid"> + <thead> + <tr> + <th>No.</th> + <th>Sample Name</th> + %if grid_index == 0: + <th>State</th> + %endif + %for index, field in fields_dict.items(): + <th> + ${field['label']} + <div class="toolParamHelp" style="clear: both;"> + <i>${field['helptext']}</i> + </div> + </th> + %endfor + <th></th> + </tr> + <thead> + <tbody> + <% + request.refresh() + %> + %for sample_index, sample in enumerate(current_samples): + %if edit_mode: + <tr> + <td>${sample_index+1}</td> + ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} + <td> + %if request.unsubmitted() and grid_index == 0: + <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %else: + <tr> + <td>${sample_index+1}</td> + %if sample_index in range(len(request.samples)): + ${render_sample( sample_index, request.samples[sample_index], grid_index, fields_dict )} + %else: + ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} + %endif + <td> + %if request.unsubmitted() and grid_index == 0: + <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %endif + %endfor + </tbody> + </table> +</%def> + <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: - <table class="grid"> - <thead> - <tr> - <th>No.</th> - <th>Sample Name</th> - <th>State</th> - %for field_index, field in enumerate(request.type.sample_form.fields): - <th> - ${field['label']} - <div class="toolParamHelp" style="clear: both;"> - <i>${field['helptext']}</i> - </div> - </th> - %endfor - <th></th> - </tr> - <thead> - <tbody> - <% - request.refresh() - %> - %for sample_index, sample in enumerate(current_samples): - %if edit_mode: - <tr> - <td>${sample_index+1}</td> - ${render_sample_form( sample_index, sample[0], sample[1])} - </tr> - %else: - <tr> - <td>${sample_index+1}</td> - %if sample_index in range(len(request.samples)): - ${render_sample( sample_index, request.samples[sample_index] )} - %else: - ${render_sample_form( sample_index, sample[0], sample[1])} - %endif - <td> - %if request.unsubmitted(): - <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> - <img src="${h.url_for('/static/images/delete_icon.png')}" /> - <span></span></a> - %endif - </td> - </tr> - %endif - %endfor - </tbody> - </table> + %if not request.type.sample_form.layout: + ${render_grid( 0, "", request.type.sample_form.fields_of_grid( None ) )} + %else: + %for grid_index, grid_name in enumerate(request.type.sample_form.layout): + ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_name ) )} + %endfor + %endif %else: <label>There are no samples.</label> %endif diff -r 1fb29bd2725a -r c40962280e72 templates/admin/requests/view_request_type.mako --- a/templates/admin/requests/view_request_type.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/admin/requests/view_request_type.mako Wed Sep 16 12:39:57 2009 -0400 @@ -11,7 +11,7 @@ <div class="toolForm"> <div class="toolFormTitle">View request type details</div> <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='request_type', save_changes=True, create=False, id=request_type.id, num_states=num_states )}" method="post" > + <form name="library"> <div class="form-row"> <label>Name</label> ${request_type.name} diff -r 1fb29bd2725a -r c40962280e72 templates/requests/new_request.mako --- a/templates/requests/new_request.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/requests/new_request.mako Wed Sep 16 12:39:57 2009 -0400 @@ -58,9 +58,9 @@ <div class="form-row"> <label>${field['label']}</label> ${field['widget'].get_html()} - %if field['label'] == 'Data library' and new_library: - ${new_library.get_html()} - %endif + ##%if field['label'] == 'Data library' and new_library: + ## ${new_library.get_html()} + ##%endif <div class="toolParamHelp" style="clear: both;"> ${field['helptext']} </div> diff -r 1fb29bd2725a -r c40962280e72 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Wed Sep 16 11:27:50 2009 -0400 +++ b/templates/requests/show_request.mako Wed Sep 16 12:39:57 2009 -0400 @@ -26,18 +26,40 @@ -<%def name="render_sample_form( index, sample_name, sample_values )"> - <td> - <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> - <div class="toolParamHelp" style="clear: both;"> - <i>${' (required)' }</i> - </div> - </td> - <td> - </td> - %for field_index, field in enumerate(request.type.sample_form.fields): +<%def name="render_sample_form( index, sample_name, sample_values, grid_index, fields_dict )"> + %if grid_index == 0: <td> - <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/> + <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/> + <div class="toolParamHelp" style="clear: both;"> + <i>${' (required)' }</i> + </div> + </td> + <td> + </td> + %else: + <td> + ${sample_name} + </td> + %endif + %for field_index, field in fields_dict.items(): + <td> + %if field['type'] == 'TextField': + <input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> + %elif field['type'] == 'SelectField': + <select name="sample_${index}_field_${field_index}" last_selected_value="2"> + %for option_index, option in enumerate(field['selectlist']): + %if option == sample_values[field_index]: + <option value="${option}" selected>${option}</option> + %else: + <option value="${option}">${option}</option> + %endif + %endfor + </select> + %elif field['type'] == 'CheckboxField': + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %elif field['type'] == 'NumberField': + <input type=int name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/> + %endif <div class="toolParamHelp" style="clear: both;"> <i>${'('+field['required']+')' }</i> </div> @@ -45,18 +67,20 @@ %endfor </%def> -<%def name="render_sample( index, sample )"> +<%def name="render_sample( index, sample, grid_index, fields_dict )"> <td> ${sample.name} </td> - <td> - %if sample.request.unsubmitted(): - Unsubmitted - %else: - <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> - %endif - </td> - %for field_index, field in enumerate(request.type.sample_form.fields): + %if grid_index == 0: + <td> + %if sample.request.unsubmitted(): + Unsubmitted + %else: + <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> + %endif + </td> + %endif + %for field_index, field in fields_dict.items(): <td> %if sample.values.content[field_index]: ${sample.values.content[field_index]} @@ -105,65 +129,81 @@ </div> </div> +<%def name="render_grid( grid_index, grid_name, fields_dict )"> + %if grid_name: + <div class="toolFormTitle">${grid_name}</div> + %endif + <div style="clear: both"></div> + <table class="grid"> + <thead> + <tr> + <th>No.</th> + <th>Sample Name</th> + %if grid_index == 0: + <th>State</th> + %endif + %for index, field in fields_dict.items(): + <th> + ${field['label']} + <div class="toolParamHelp" style="clear: both;"> + <i>${field['helptext']}</i> + </div> + </th> + %endfor + <th></th> + </tr> + <thead> + <tbody> + <% + request.refresh() + %> + %for sample_index, sample in enumerate(current_samples): + %if edit_mode: + <tr> + <td>${sample_index+1}</td> + ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} + <td> + %if request.unsubmitted() and grid_index == 0: + <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %else: + <tr> + <td>${sample_index+1}</td> + %if sample_index in range(len(request.samples)): + ${render_sample( sample_index, request.samples[sample_index], grid_index, fields_dict )} + %else: + ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)} + %endif + <td> + %if request.unsubmitted() and grid_index == 0: + <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> + <img src="${h.url_for('/static/images/delete_icon.png')}" /> + <span></span></a> + %endif + </td> + </tr> + %endif + %endfor + </tbody> + </table> +</%def> + <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request' )}" enctype="multipart/form-data" method="post" > <div class="form-row"> - %if current_samples: - <table class="grid"> - <thead> - <tr> - <th>No.</th> - <th>Sample Name</th> - <th>State</th> - %for field_index, field in enumerate(request.type.sample_form.fields): - <th> - ${field['label']} - <div class="toolParamHelp" style="clear: both;"> - <i>${field['helptext']}</i> - </div> - </th> - %endfor - <th></th> - </tr> - <thead> - <tbody> - <% - request.refresh() - %> - %for sample_index, sample in enumerate(current_samples): - %if edit_mode: - <tr> - <td>${sample_index+1}</td> - ${render_sample_form( sample_index, sample[0], sample[1])} - <td> - %if request.unsubmitted(): - <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> - <img src="${h.url_for('/static/images/delete_icon.png')}" /> - <span></span></a> - %endif - </td> - </tr> - %else: - <tr> - <td>${sample_index+1}</td> - %if sample_index in range(len(request.samples)): - ${render_sample( sample_index, request.samples[sample_index] )} - %else: - ${render_sample_form( sample_index, sample[0], sample[1])} - %endif - <td> - %if request.unsubmitted(): - <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}"> - <img src="${h.url_for('/static/images/delete_icon.png')}" /> - <span></span></a> - %endif - </td> - </tr> - %endif - %endfor - </tbody> - </table> + %if current_samples: + %if not request.type.sample_form.layout: + ${render_grid( 0, "", request.type.sample_form.fields_of_grid( None ) )} + %else: + %for grid_index, grid_name in enumerate(request.type.sample_form.layout): + ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_name ) )} + %endfor + %endif %else: <div class="form-row"> <label>There are no samples.</label> diff -r 1fb29bd2725a -r c40962280e72 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Sep 16 11:27:50 2009 -0400 +++ b/test/base/twilltestcase.py Wed Sep 16 12:39:57 2009 -0400 @@ -972,15 +972,13 @@ self.home() # Form stuff - def create_form( self, name='Form One', desc='This is Form One', num_fields=1 ): + def create_form( self, name, desc, formtype, num_fields=1 ): """ Create a new form definition. Testing framework is still limited to only testing one instance for each repeat. This has to do with the 'flat' nature of defining test param values. Using same-named parameters down different branches (having different scope in the tool) cannot be properly tested when they both exist at the same time. - TODO: RC: create an edit_form() method that will test the addition of a new field - of a specified type. """ # TODO: RC: enhance this so that all supported field types can be passed in # and tested. If nothing is passed, all fields are TextField. @@ -988,7 +986,8 @@ self.visit_url( "%s/forms/new" % self.url ) self.check_page_for_string( 'Create a new form definition' ) tc.fv( "1", "name", name ) # form field 1 is the field named name... - tc.fv( "1", "description", desc ) # form field 1 is the field named name... + tc.fv( "1", "description", desc ) # form field 1 is the field named desc... + tc.fv( "1", "form_type_selectbox", formtype ) tc.submit( "create_form_button" ) for index in range( num_fields ): field_name = 'field_name_%i' % index @@ -1053,7 +1052,7 @@ # Requests stuff def create_request_type( self, name, desc, request_form_id, sample_form_id, states ): self.home() - self.visit_url( "%s/admin/request_type?create=True" % self.url ) + self.visit_url( "%s/requests_admin/request_type?create=True" % self.url ) self.check_page_for_string( 'Create a new request type' ) tc.fv( "1", "name", name ) tc.fv( "1", "description", desc ) @@ -1067,13 +1066,14 @@ tc.fv("1", "state_desc_%i" % index, state[1]) tc.submit( "save_request_type" ) self.check_page_for_string( "Request type <b>%s</b> has been created" % name ) - def create_request( self, request_type_id, name, desc, library_id, fields ): + def create_request( self, request_type_id, name, desc, library_id, folder_id, fields ): self.home() self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) ) self.check_page_for_string( 'Add a new request' ) tc.fv( "1", "name", name ) tc.fv( "1", "desc", desc ) tc.fv( "1", "library_id", str(library_id) ) + #tc.fv( "1", "folder_id", str(folder_id) ) for index, field_value in enumerate(fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "create_request_button" ) @@ -1088,13 +1088,14 @@ for index, field_value in enumerate(fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "create_request_button" ) - def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_fields): + def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_folder_id, new_fields): self.home() self.visit_url( "%s/requests/edit?request_id=%i&show=True" % (self.url, request_id) ) self.check_page_for_string( 'Edit request "%s"' % name ) tc.fv( "1", "name", new_name ) tc.fv( "1", "desc", new_desc ) tc.fv( "1", "library_id", str(new_library_id) ) + tc.fv( "1", "folder_id", str(new_folder_id) ) for index, field_value in enumerate(new_fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "save_changes_request_button" ) diff -r 1fb29bd2725a -r c40962280e72 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Wed Sep 16 11:27:50 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Wed Sep 16 12:39:57 2009 -0400 @@ -41,14 +41,17 @@ global form_one_name name = form_one_name desc = "This is Form One's description" - self.create_form( name=name, desc=desc ) + formtype = 'Sequencing Request Form' + self.create_form( name=name, desc=desc, formtype=formtype ) self.home() self.visit_page( 'forms/manage' ) self.check_page_for_string( name ) self.check_page_for_string( desc ) + self.check_page_for_string( formtype ) # Get the form_definition object for later tests form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name, - galaxy.model.FormDefinition.table.c.desc==desc ) ).all()[-1] + galaxy.model.FormDefinition.table.c.desc==desc, + galaxy.model.FormDefinition.table.c.type==formtype ) ).all()[-1] assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name # edit form & add few more fields new_name = "Request Form (Renamed)" @@ -86,15 +89,18 @@ global form_two_name name = form_two_name desc = "This is Form One's description" - self.create_form( name=name, desc=desc ) + formtype = 'Sequencing Sample Form' + self.create_form( name=name, desc=desc, formtype=formtype ) self.home() self.visit_page( 'forms/manage' ) self.check_page_for_string( name ) self.check_page_for_string( desc ) + self.check_page_for_string( formtype ) def test_020_create_request_type( self ): """Testing creating a new requestype""" request_form = get_latest_form(form_one_name) sample_form = get_latest_form(form_two_name) + print request_form.id, sample_form.id self.create_request_type(request_type_name, "test request type", str(request_form.id), str(sample_form.id), sample_states ) global request_type @@ -147,6 +153,17 @@ # Role one members are: admin_user, regular_user1. Each of these users will be permitted to # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items. self.set_library_permissions( str( library_one.id ), library_one.name, str( regular_user1_private_role.id ), permissions_in, permissions_out ) + # create a folder in the library + root_folder = library_one.root_folder + name = "Folder One" + self.add_folder( str( library_one.id ), str( root_folder.id ), name=name, description='' ) + global folder_one + folder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id, + galaxy.model.LibraryFolder.table.c.name==name ) ).first() + assert folder_one is not None, 'Problem retrieving library folder named "%s" from the database' % name + self.home() + self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( name ) # create address #self.create_address( user_address1 ) #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] ) @@ -175,7 +192,7 @@ fields = ['field one value', 'field two value', str(user_address.id)] # create the request request_name, request_desc = 'Request One', 'Request One Description' - self.create_request(request_type.id, request_name, request_desc, library_one.id, fields) + self.create_request(request_type.id, request_name, request_desc, library_one.id, folder_one.id, fields) self.check_page_for_string( request_name ) self.check_page_for_string( request_desc ) global request_one @@ -195,7 +212,7 @@ self.check_page_for_string( field_value ) # edit this request fields = ['field one value (editted)', 'field two value (editted)', str(user_address.id)] - self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, fields) + self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) request_one.refresh() self.check_page_for_string( request_name+' (Renamed)' ) self.check_page_for_string( request_desc+' (Re-described)' )

1 0

[hg] galaxy 2692: Fix maf_utilities compatibility with python 2....
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ba884f1a6b81 changeset: 2692:ba884f1a6b81 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 15 10:15:42 2009 -0400 description: Fix maf_utilities compatibility with python 2.4; STRING.startswith() accepting a tuple was introduced in python 2.5. 1 file(s) affected in this change: lib/galaxy/tools/util/maf_utilities.py diffs (23 lines): diff -r 40c5e1853a66 -r ba884f1a6b81 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Mon Sep 14 17:03:17 2009 -0400 +++ b/lib/galaxy/tools/util/maf_utilities.py Tue Sep 15 10:15:42 2009 -0400 @@ -403,7 +403,7 @@ else: blocks.append( ( score, idx, offset ) ) - gap_chars_tuple = tuple( GAP_CHARS ) + #gap_chars_tuple = tuple( GAP_CHARS ) gap_chars_str = ''.join( GAP_CHARS ) #Loop through ordered blocks and layer by increasing score for block_dict in blocks: for block in iter_blocks_split_by_species( block_dict[1].get_at_offset( block_dict[2] ) ): #need to handle each occurance of sequence in block seperately @@ -415,7 +415,8 @@ #we should trim gaps from both sides, since these are not positions in this species genome (sequence) text = text.rstrip( gap_chars_str ) gap_offset = 0 - while text.startswith( gap_chars_tuple ): + while True in [ text.startswith( gap_char ) for gap_char in GAP_CHARS ]: #python2.4 doesn't accept a tuple for .startswith() + #while text.startswith( gap_chars_tuple ): gap_offset += 1 text = text[1:] if not text:

1 0

[hg] galaxy 2698: Updated BWA wrapper tool: replaced threads opt...
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14d54c9dbd59 changeset: 2698:14d54c9dbd59 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Sep 16 11:14:39 2009 -0400 description: Updated BWA wrapper tool: replaced threads option to hard-coded value, changed output and test file output datatype to sam, changed test file names to standard, better cleanup of temp files, added dbkey parameter and exec_before_job method to set it. Also changed name of a FASTQ Conversions tool test file 17 file(s) affected in this change: test-data/bwa_wrapper_in1.fastq test-data/bwa_wrapper_in2.fastq test-data/bwa_wrapper_in3.fastq test-data/bwa_wrapper_in4.fastq test-data/bwa_wrapper_in5.fastq test-data/bwa_wrapper_in6.fastq test-data/bwa_wrapper_out0.sam test-data/bwa_wrapper_out0b.sam test-data/bwa_wrapper_out1.sam test-data/bwa_wrapper_out2.sam test-data/bwa_wrapper_out3.sam test-data/bwa_wrapper_out4.sam test-data/fastq_conv_in1.fastq tools/next_gen_conversion/fastq_conversions.xml tools/sr_mapping/bwa_wrapper.py tools/sr_mapping/bwa_wrapper.xml tools/sr_mapping/bwa_wrapper_code.py diffs (1880 lines): diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in1.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in2.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in3.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in3.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in4.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in4.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in5.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in5.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/2 +ACGCTCCTTTAAAATATC ++/2 +IIIII$%*$G$A31I&&B diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_in6.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in6.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/1 +GGACTCAGATAGTAATCC ++/1 +II#IIIIIII$5+.(9II diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out0.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,2 @@ +@SQ SN:PHIX174 LN:5386 +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out0b.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0b.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,145 @@ +@SQ SN:phiX LN:5386 +1831_573_1004 0 phiX 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +1831_573_1219 16 phiX 2202 37 1S33M * 0 0 TACGTCACCTTATCAGTCCAATTTAAATTACACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1242 0 phiX 648 37 33M1S * 0 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATCC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) +1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +1831_573_1448 16 phiX 2563 25 1S33M * 0 0 CGAAGTAACGTAAGTCTACCTATGTAGACAGTTG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1490 0 phiX 1767 25 33M1S * 0 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +1831_573_1647 16 phiX 1118 37 1S33M * 0 0 ACTGAGGAAGCTCTACCTGCGGCAACCGCGAGAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1684 16 phiX 3696 37 1S33M * 0 0 ATCACGACTCCAACTGAATCAAGTAGTCGTTTGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 +1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +1831_574_109 0 phiX 3729 37 33M1S * 0 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGCT VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_148 16 phiX 2369 37 1S33M * 0 0 GATCCAAAAGACGAATCCTCAAATTAGTACAAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# +1831_574_243 0 phiX 2129 37 33M1S * 0 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGCA ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +1831_574_575 16 phiX 4006 37 1S33M * 0 0 CTTACAGTGCGACTAATAAAACTGAAACTCGCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_592 16 phiX 2950 37 1S33M * 0 0 TCGCCATAACGAAGACGAGAACGACCACCGCGGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- +1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +1831_574_734 16 phiX 5263 25 1S33M * 0 0 CCTCTCTACTCTAACTCCGACCCTTTTCAATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_824 16 phiX 3997 37 1S33M * 0 0 ATGGGAAGACTTACAGTGCGACTAATAAAACTGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ +1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +1831_574_1194 0 phiX 1136 37 33M1S * 0 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTG \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1204 16 phiX 1445 25 1S33M * 0 0 TGGATTACTCGAATTAGTTCTACTACGAGCAATA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +1831_574_1591 16 phiX 5118 37 1S33M * 0 0 CTTCGACAAGTCTTAGTCTTACTCGGCGTTGAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1624 16 phiX 4058 37 1S33M * 0 0 CATAACTCCGAACACCGTAAAGATGAGAAAGAGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +1831_574_1903 0 phiX 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1961 0 phiX 3555 25 33M1S * 0 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTTA TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_54 16 phiX 3587 37 1S33M * 0 0 TAAGGTTCGTTGTCGTCCAAAGGCTCTAATACGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +1831_575_197 16 phiX 4861 37 1S33M * 0 0 CCGAACGTTTTATGCACCGGAATACCAATGTCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. +1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +1831_575_444 16 phiX 5098 37 1S33M * 0 0 TTCGACAGCGATGAAGGGTTCTTCGACAAGTCTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +1831_575_569 0 phiX 5043 25 33M1S * 0 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAAT IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_622 0 phiX 2485 37 33M1S * 0 0 GTTTTACAGACACCTAAAGCTACATCGTCAACGC ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +1831_575_663 16 phiX 1554 25 1S33M * 0 0 TGCTGAAGATGGTGTAGATAACTGTAATACCCAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& +1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# +1831_575_938 16 phiX 1133 37 1S33M * 0 0 TCTGCGGCAACCGCGAGAGGCAGAAAGAGGTAAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_970 16 phiX 232 37 1S33M * 0 0 GCTCCTCTTCACCGAATTATACGAACCGTGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +1831_575_1138 0 phiX 1913 37 33M1S * 0 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCTC VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1157 16 phiX 3736 25 1S33M * 0 0 GTCGCCATACCGAGAAGAGTATAACCGCGATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1180 0 phiX 4169 37 33M1S * 0 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGTA ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +1831_575_1302 16 phiX 5202 37 1S33M * 0 0 GGAATGGTTCGACCCAATGCTGCGCTGCGGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1310 16 phiX 1612 37 1S33M * 0 0 AATGACTGGTTCTTGCACTAATGAAGTACGTCGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1321 0 phiX 2664 37 33M1S * 0 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACG ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1373 16 phiX 4221 37 1S33M * 0 0 TAGACTGCAAGCACTACTCAAACATAGACAATGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +1831_575_1436 0 phiX 3460 37 33M1S * 0 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATAC []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1442 0 phiX 3317 37 33M1S * 0 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCG \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +1831_575_1500 16 phiX 4269 37 1S33M * 0 0 GCTTAACCGTGTTACGATGTTACACGAGGGGGTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1535 16 phiX 1225 37 1S33M * 0 0 GAGTGCAAATACCACTTGTCACCTAATTCAAGTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +1831_576_32 16 phiX 988 25 1S33M * 0 0 TAACTCCTATTTAATACAGATTATAAGTTTGACC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? +1831_576_86 16 phiX 2981 37 1S33M * 0 0 TGTACAGATTTAACAAACCTCCGCCAGTTTTTCG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +1831_576_266 16 phiX 280 37 1S33M * 0 0 ATCTATACTCAGTGTAAAACAAGTACCATCTCTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_327 16 phiX 4517 25 1S33M * 0 0 TATGATAAGTCGCAAACTACTTACGTTACGCTGT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:1G31 +1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( +1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +1831_576_519 16 phiX 1625 25 1S33M * 0 0 GGCACTAATGAAGTACGTCGCAATGGCACTACAA XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:25A7 +1831_576_603 16 phiX 1576 37 1S33M * 0 0 GGTAATACCCAGACGTTCGACGAATACGATTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_655 16 phiX 3292 37 1S33M * 0 0 CAACGACGACGTAAAGGACTCGAATTACGAACCC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### +1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +1831_576_815 0 phiX 5186 37 33M1S * 0 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_882 0 phiX 5053 37 33M1S * 0 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACTG Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_898 0 phiX 518 37 33M1S * 0 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTGT ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_923 0 phiX 1050 37 33M1S * 0 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCG MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +1831_576_1131 16 phiX 4061 37 1S33M * 0 0 TACTCCGAACACCGTAAAGATGAGAAAGAGTTAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +1831_576_1289 16 phiX 1899 37 1S33M * 0 0 AAAGTCATGGAATTGCGATTTCCACGAAACTGAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +1831_576_1367 0 phiX 1839 37 33M1S * 0 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTCT ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1416 0 phiX 4522 37 33M1S * 0 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTCC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +1831_576_1605 0 phiX 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +1831_576_1729 16 phiX 5194 37 1S33M * 0 0 TATTAGGTTGAATGGTTCGACCCAATGCTGCGCT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 +1831_576_1982 16 phiX 5024 37 1S33M * 0 0 TATTGTTTTTCAGTCTATACCTGGAACGACGATT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +1831_577_40 0 phiX 2772 25 33M1S * 0 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGGT JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 +1831_577_133 16 phiX 1714 37 1S33M * 0 0 CGTACGCGAGATTAGAGACCCGTAGACCGATACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +1831_577_281 16 phiX 4577 37 1S33M * 0 0 TAAAACTGTGAGAGTGCAACCGACTGCTGGCTAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_288 0 phiX 3201 25 33M1S * 0 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATA SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_322 16 phiX 458 37 1S33M * 0 0 CAAGACGGCAAAACCTAAATTGGCTTCTACTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_362 0 phiX 2153 37 33M1S * 0 0 CTTATTCGCCACCATGATTATGACCAGTGTTTCA ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_382 16 phiX 4686 37 1S33M * 0 0 TCCAGCGTTCCGATTACTAAGTGTGCGGCTGACG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_464 0 phiX 2126 25 33M1S * 0 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATTG ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_488 16 phiX 4948 37 1S33M * 0 0 GCCGGACAACTACGATTTCCACTCGGCGAATTTC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +1831_577_545 0 phiX 1711 37 33M1S * 0 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_559 0 phiX 3840 25 33M1S * 0 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAAG ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +1831_577_637 0 phiX 4247 37 33M1S * 0 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACAA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +1831_577_692 0 phiX 3905 37 33M1S * 0 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTCA WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out1.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,145 @@ +@SQ SN:PHIX174 LN:5386 +1831_573_1004 0 PHIX174 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +1831_573_1219 16 PHIX174 2202 37 1S33M * 0 0 TACGTCACCTTATCAGTCCAATTTAAATTACACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1242 0 PHIX174 648 37 33M1S * 0 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATCC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) +1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +1831_573_1448 16 PHIX174 2563 25 1S33M * 0 0 CGAAGTAACGTAAGTCTACCTATGTAGACAGTTG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1490 0 PHIX174 1767 25 33M1S * 0 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +1831_573_1647 16 PHIX174 1118 37 1S33M * 0 0 ACTGAGGAAGCTCTACCTGCGGCAACCGCGAGAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1684 16 PHIX174 3696 37 1S33M * 0 0 ATCACGACTCCAACTGAATCAAGTAGTCGTTTGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 +1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +1831_574_109 0 PHIX174 3729 37 33M1S * 0 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGCT VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_148 16 PHIX174 2369 37 1S33M * 0 0 GATCCAAAAGACGAATCCTCAAATTAGTACAAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# +1831_574_243 0 PHIX174 2129 37 33M1S * 0 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGCA ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +1831_574_575 16 PHIX174 4006 37 1S33M * 0 0 CTTACAGTGCGACTAATAAAACTGAAACTCGCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_592 16 PHIX174 2950 37 1S33M * 0 0 TCGCCATAACGAAGACGAGAACGACCACCGCGGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- +1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +1831_574_734 16 PHIX174 5263 25 1S33M * 0 0 CCTCTCTACTCTAACTCCGACCCTTTTCAATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_824 16 PHIX174 3997 37 1S33M * 0 0 ATGGGAAGACTTACAGTGCGACTAATAAAACTGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ +1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +1831_574_1194 0 PHIX174 1136 37 33M1S * 0 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTG \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1204 16 PHIX174 1445 25 1S33M * 0 0 TGGATTACTCGAATTAGTTCTACTACGAGCAATA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +1831_574_1591 16 PHIX174 5118 37 1S33M * 0 0 CTTCGACAAGTCTTAGTCTTACTCGGCGTTGAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1624 16 PHIX174 4058 37 1S33M * 0 0 CATAACTCCGAACACCGTAAAGATGAGAAAGAGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +1831_574_1903 0 PHIX174 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1961 0 PHIX174 3555 25 33M1S * 0 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTTA TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_54 16 PHIX174 3587 37 1S33M * 0 0 TAAGGTTCGTTGTCGTCCAAAGGCTCTAATACGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +1831_575_197 16 PHIX174 4861 37 1S33M * 0 0 CCGAACGTTTTATGCACCGGAATACCAATGTCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. +1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +1831_575_444 16 PHIX174 5098 37 1S33M * 0 0 TTCGACAGCGATGAAGGGTTCTTCGACAAGTCTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +1831_575_569 0 PHIX174 5043 25 33M1S * 0 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAAT IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_622 0 PHIX174 2485 37 33M1S * 0 0 GTTTTACAGACACCTAAAGCTACATCGTCAACGC ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +1831_575_663 16 PHIX174 1554 25 1S33M * 0 0 TGCTGAAGATGGTGTAGATAACTGTAATACCCAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& +1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# +1831_575_938 16 PHIX174 1133 37 1S33M * 0 0 TCTGCGGCAACCGCGAGAGGCAGAAAGAGGTAAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_970 16 PHIX174 232 37 1S33M * 0 0 GCTCCTCTTCACCGAATTATACGAACCGTGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +1831_575_1138 0 PHIX174 1913 37 33M1S * 0 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCTC VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1157 16 PHIX174 3736 25 1S33M * 0 0 GTCGCCATACCGAGAAGAGTATAACCGCGATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1180 0 PHIX174 4169 37 33M1S * 0 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGTA ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +1831_575_1302 16 PHIX174 5202 37 1S33M * 0 0 GGAATGGTTCGACCCAATGCTGCGCTGCGGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1310 16 PHIX174 1612 37 1S33M * 0 0 AATGACTGGTTCTTGCACTAATGAAGTACGTCGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1321 0 PHIX174 2664 37 33M1S * 0 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACG ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1373 16 PHIX174 4221 37 1S33M * 0 0 TAGACTGCAAGCACTACTCAAACATAGACAATGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +1831_575_1436 0 PHIX174 3460 37 33M1S * 0 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATAC []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1442 0 PHIX174 3317 37 33M1S * 0 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCG \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +1831_575_1500 16 PHIX174 4269 37 1S33M * 0 0 GCTTAACCGTGTTACGATGTTACACGAGGGGGTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1535 16 PHIX174 1225 37 1S33M * 0 0 GAGTGCAAATACCACTTGTCACCTAATTCAAGTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +1831_576_32 16 PHIX174 988 25 1S33M * 0 0 TAACTCCTATTTAATACAGATTATAAGTTTGACC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? +1831_576_86 16 PHIX174 2981 37 1S33M * 0 0 TGTACAGATTTAACAAACCTCCGCCAGTTTTTCG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +1831_576_266 16 PHIX174 280 37 1S33M * 0 0 ATCTATACTCAGTGTAAAACAAGTACCATCTCTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_327 16 PHIX174 4517 37 1S33M * 0 0 TATGATAAGTCGCAAACTACTTACGTTACGCTGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( +1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +1831_576_519 16 PHIX174 1625 37 1S33M * 0 0 GGCACTAATGAAGTACGTCGCAATGGCACTACAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_603 16 PHIX174 1576 37 1S33M * 0 0 GGTAATACCCAGACGTTCGACGAATACGATTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_655 16 PHIX174 3292 37 1S33M * 0 0 CAACGACGACGTAAAGGACTCGAATTACGAACCC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### +1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +1831_576_815 0 PHIX174 5186 37 33M1S * 0 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_882 0 PHIX174 5053 37 33M1S * 0 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACTG Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_898 0 PHIX174 518 37 33M1S * 0 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTGT ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_923 0 PHIX174 1050 37 33M1S * 0 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCG MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +1831_576_1131 16 PHIX174 4061 37 1S33M * 0 0 TACTCCGAACACCGTAAAGATGAGAAAGAGTTAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +1831_576_1289 16 PHIX174 1899 37 1S33M * 0 0 AAAGTCATGGAATTGCGATTTCCACGAAACTGAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +1831_576_1367 0 PHIX174 1839 37 33M1S * 0 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTCT ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1416 0 PHIX174 4522 37 33M1S * 0 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTCC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +1831_576_1605 0 PHIX174 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +1831_576_1729 16 PHIX174 5194 37 1S33M * 0 0 TATTAGGTTGAATGGTTCGACCCAATGCTGCGCT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 +1831_576_1982 16 PHIX174 5024 37 1S33M * 0 0 TATTGTTTTTCAGTCTATACCTGGAACGACGATT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +1831_577_40 0 PHIX174 2772 25 33M1S * 0 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGGT JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 +1831_577_133 16 PHIX174 1714 37 1S33M * 0 0 CGTACGCGAGATTAGAGACCCGTAGACCGATACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +1831_577_281 16 PHIX174 4577 37 1S33M * 0 0 TAAAACTGTGAGAGTGCAACCGACTGCTGGCTAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_288 0 PHIX174 3201 25 33M1S * 0 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATA SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_322 16 PHIX174 458 37 1S33M * 0 0 CAAGACGGCAAAACCTAAATTGGCTTCTACTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_362 0 PHIX174 2153 37 33M1S * 0 0 CTTATTCGCCACCATGATTATGACCAGTGTTTCA ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_382 16 PHIX174 4686 37 1S33M * 0 0 TCCAGCGTTCCGATTACTAAGTGTGCGGCTGACG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_464 0 PHIX174 2126 25 33M1S * 0 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATTG ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_488 16 PHIX174 4948 37 1S33M * 0 0 GCCGGACAACTACGATTTCCACTCGGCGAATTTC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +1831_577_545 0 PHIX174 1711 37 33M1S * 0 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_559 0 PHIX174 3840 25 33M1S * 0 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAAG ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +1831_577_637 0 PHIX174 4247 37 33M1S * 0 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACAA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +1831_577_692 0 PHIX174 3905 37 33M1S * 0 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTCA WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out2.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,97 @@ +@SQ SN:PHIX174 LN:5386 +1378_11_329 77 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ +1378_11_329 141 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# +1378_17_1788 77 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### +1378_17_1788 141 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$###### +1378_25_2035 77 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% +1378_25_2035 141 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# +1378_28_770 77 * 0 0 * * 0 0 GGTTGGGAGTTGGCGCGCGTGGTT ###$##%%$####%#%$#%%#($$ +1378_28_770 141 * 0 0 * * 0 0 CTGCTATGCCGGCCGCCTGCCCCT %##(#$$#%$#$%###$%%$##$# +1378_33_1945 77 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG .6;?;55697>8779457986264 +1378_33_1945 141 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG +9;64287788752796/576352 +1378_34_789 77 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#& +1378_34_789 141 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$ +1378_35_263 77 * 0 0 * * 0 0 GGCGGGGGGGGGGGGGGGGGGGGG $%%&,)3/)%$-6'$&5&#$''5. +1378_35_263 141 * 0 0 * * 0 0 GGGCGGGGGGCGGCGGGGGGGGGG ),,#%'$)'-(%&%'%',%%&&(& +1378_43_186 77 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#' +1378_43_186 141 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$# +1378_51_1671 77 * 0 0 * * 0 0 GGTGTTGTTCGGATGTAGCGTGGG ##%$$####$########$##0## +1378_51_1671 141 * 0 0 * * 0 0 TGGGTAGGTGCGGCTCTTGCGGTC ##$#$%###%%#%#$##$$##### +1378_56_324 77 * 0 0 * * 0 0 GCTGGGTGATCTAAGGAATGTAAT #$#####$$$#$$$$##%###*(# +1378_56_324 141 * 0 0 * * 0 0 AGGCTTGGATTGTTGCGCTGACCT /+#**###%%##%#####$$$#$# +1378_56_773 77 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$ +1378_56_773 141 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$ +1378_62_2027 77 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&# +1378_62_2027 141 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'# +1378_62_2029 77 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%# +1378_62_2029 141 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$### +1378_67_1795 77 * 0 0 * * 0 0 CGTGCCAACGACCGTCCTACGGAG @@.?7@@@.@:@A<<>>=>70<@7 +1378_67_1795 141 * 0 0 * * 0 0 TAGTGGGCTAGTCCGGGATCTACC B@C2@@?;-@@1>'A@@91@.@1' +1378_68_466 77 * 0 0 * * 0 0 GTGTCATCTGAGGTAAAGCATTGT /##$09#$#.=$#$76+$%1'### +1378_68_466 141 * 0 0 * * 0 0 GTGATCGTCGGTGCCAGTCCCTGT #(%)+##$#$#%#+$%##$##### +1378_68_1692 77 * 0 0 * * 0 0 TGTTCGATTTAGGTCTTGCCTCGC ###%%$%%##%$#$##$###$$#$ +1378_68_1692 141 * 0 0 * * 0 0 GGTCTTCTGGGCACGGGCCAAGTT ###)%'&%##$###%#######$# +1378_80_664 77 * 0 0 * * 0 0 TGTCTGCGTTGTATCTCTGGTGTA %##%,%$$#&$$###$#$%##'%# +1378_80_664 141 * 0 0 * * 0 0 CTGCTTTGATCCCCGGTGGAGCAC 7#%###$$6#######$##$$$## +1378_85_1786 77 * 0 0 * * 0 0 CCCTAGGAGCGTATACCGGACGAG ,'&/%/@,&1,&'/)&,6&&1)(( +1378_85_1786 141 * 0 0 * * 0 0 ATACTATGTCGATCTGTAAAAAAA )&.)#3%(a)$&%-,2#&+.-%0&./ +1378_86_1011 77 * 0 0 * * 0 0 AGGCGATGGGATATTATTTTACTT :$###)%##$9$###1$$#$2### +1378_86_1011 141 * 0 0 * * 0 0 CTACGTTATTGCTCTGTTTGTCCT ######$%##$$$%###%#$#### +1378_86_1789 77 * 0 0 * * 0 0 GGCCAGGTACTAATAAATTCAACA 1.51/&%#'$,*?%#6&0$$5,20 +1378_86_1789 141 * 0 0 * * 0 0 CGAATATCCCCTGGTTTAGAAGTA 61?1;@/>@<=/(.7'(<5@=%$= +1378_91_1596 77 * 0 0 * * 0 0 GCTTTTTCATTCGGTGCCTTTGGA '>%/3%=()8'#.%?50$&5>%)% +1378_91_1596 141 * 0 0 * * 0 0 TTAGCGGTTGACTATCTGCTGACA *&+'#9'(%*'#//,&<),/)'*# +1378_94_1595 77 * 0 0 * * 0 0 GCGGGTTAACCCAGTACCTCTGGC ,8@6'>8<76>@@(->9)7'*941 +1378_94_1595 141 * 0 0 * * 0 0 CGTGCGACAGCCCATGTTTTCAGA -=..5,3826&*+.+#+#%%6;%# +1378_95_1039 77 * 0 0 * * 0 0 GTTCTGTGCCAGGTGAGGTACGGA &##,./#$&)6##+,'#$$0(##$ +1378_95_1039 141 * 0 0 * * 0 0 CGGCGTCCATCTTCGCCTTGAGAT $##.#$##$$#%$#$%%$###$)$ +1378_95_1767 77 * 0 0 * * 0 0 CTAATTGACCGGGCAAGCTATTAA ',,2'(10/>:=/7).3&%6&)&6 +1378_95_1767 141 * 0 0 * * 0 0 ACACGCACCATCTGGCGGCTAACC 86<65<4<C27/$5+#;-$+#2%$ +1378_96_1037 77 * 0 0 * * 0 0 CTGCTGGGCCATTTGACTTACTCA '$#+#(##-%5##+*&###-.$$$ +1378_96_1037 141 * 0 0 * * 0 0 ATCCCCCAAGATGCCTGTTGATTG $#$'##$$$#%$$#%###+##$#$ +1378_96_1764 77 * 0 0 * * 0 0 TCTTTGTAACCCACTTAGTATTTC 4='28>.@4881B807:822>%)1 +1378_96_1764 141 * 0 0 * * 0 0 TACACCGGAACCTTGCACTAAAGC 6-9'<#+81?+*<8-=69&6;*3) +1378_98_1574 77 * 0 0 * * 0 0 AGGCGAGTGTGGGGGTTGTTTGAG +%%$#)##%##$####%###$%$# +1378_98_1574 141 * 0 0 * * 0 0 GTTCTGCCGGTGTCTGTGGCGGGC $$#+&$$####%$$$###$%#%%# +1378_107_1647 77 * 0 0 * * 0 0 GGTCTGGTTCTATGTTGGTCGACT ###'$$#$$$(#%###(#$##$%# +1378_107_1647 141 * 0 0 * * 0 0 AGGCCTACTACGCGTCATTGATAG &#$$#$(.#%#$$####&$%##($ +1378_111_829 77 * 0 0 * * 0 0 GGTCTTCTATGGTGCTAAATTAGT $##'&###$##)#%($#$%#$'%# +1378_111_829 141 * 0 0 * * 0 0 TGCGGCACTTGCTTCTTCGTATTT %#%##%#$%#$#%###$$##&#$$ +1378_111_1900 77 * 0 0 * * 0 0 GCACGCCTTTGGGCTAAGCCGTAA )$)'#%$########$'#&%$#(# +1378_111_1900 141 * 0 0 * * 0 0 TCCCCTCGCTCGGCTCTGTGCTGT $&%*$#(#)##$#'##%(##$#$% +1378_112_1483 77 * 0 0 * * 0 0 TGGAGTGGTGTGTTTGCTGAGCCA #$#)#############$#%#%'% +1378_112_1483 141 * 0 0 * * 0 0 TGTCCAGCTATGCGGCTTCCTCCT %#$+#%#&#$#####%####%$## +1378_125_1287 77 * 0 0 * * 0 0 TGACGTGGGTTGTCCCGTGAGATT ##$%%#$###$##$$#&%##$(%% +1378_125_1287 141 * 0 0 * * 0 0 TGTCTCTGGGGGGCCTGGTTAGGT $##13$'%#$###$$###$$$#&# +1378_126_468 77 * 0 0 * * 0 0 AAAAAACGGGCCGGGCGGACTAGG @@B@@@>@2>1+?:92)>@8&&<+ +1378_126_468 141 * 0 0 * * 0 0 TCTCCTGATTAGACATATCTCCGT 7>@318?=,=8@49579?..7,7) +1378_127_664 77 * 0 0 * * 0 0 TCGCTTTGCCTATGTTTGTTCGGA #%$%#&##$%#%%###$$###)-' +1378_127_664 141 * 0 0 * * 0 0 AGAGGTTGGTGTCTTGTCGCAGCT ##'#$######$$%######$$$# +1378_129_463 77 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAA ,)&20%8'(&35-***1-2&+510 +1378_129_463 141 * 0 0 * * 0 0 CCTGTGGGCCAAGCCCAATGAAAG 8),,<6(--)<()5&.&/8+;.2+ +1378_129_875 77 * 0 0 * * 0 0 GACCTTTACGTATTGGGGGTTGGC ###)###+###$##$#&%##$,#$ +1378_129_875 141 * 0 0 * * 0 0 TTTCTATGGCTTACGCTGTCTGCC #$($##%####%$#$#####$### +1378_140_1251 77 * 0 0 * * 0 0 TTTCCTTCGTGTGCGTGCGGAGTG #%#%$##$$$######.$$$%#%( +1378_140_1251 141 * 0 0 * * 0 0 ATCCTAGCGCGGTGTCTTGGGGAC #$%1#$$$##$##$#$#$##$%$$ +1378_141_809 77 * 0 0 * * 0 0 TCTCGTGGTTTCTTTTTTATGTGT ##%)##$$#####%$#$#%%#'## +1378_141_809 141 * 0 0 * * 0 0 TGTCCTCCAGTGTCTGTTGGGTGT %&,-##$$#(%###$#$$'###'# +1378_144_983 77 * 0 0 * * 0 0 GTTCGTTCGTGGTGTACGAGGGTG #(#%#####($#%##$$#%##%#) +1378_144_983 141 * 0 0 * * 0 0 AGCGCCCGGTTGGTGCGGCTCGTC -$(&%*$#*#))#$$$#%%$#$## +1378_153_270 77 * 0 0 * * 0 0 GGCCGTGTGCGGGTGTAGATTGGA %$##($######&##$&$$$$%## +1378_153_270 141 * 0 0 * * 0 0 AGTCCTTGTCCCCTGGGTTTTCCC +''$#&%$%#$##&$$($#&#$$# +1378_155_1689 77 * 0 0 * * 0 0 CGCGTTCGGACAAAGCTAGCACCT @4@@=6=@@<4:@@681@@@.24. +1378_155_1689 141 * 0 0 * * 0 0 TTGGGAGGGAGAGAGACTAGACCG ?4@@4<<??<?-@4@=4<5<?:/> +1378_157_1580 77 * 0 0 * * 0 0 GGGATTGAAGGGATGTATGCTAGG #%$&%#$$'%$%#$##*#%$$$$# +1378_157_1580 141 * 0 0 * * 0 0 TGGGCCTCGGTGCCCTTGGTCTGT #%)$##'#$$$&#####%#$#$## +1378_161_317 77 * 0 0 * * 0 0 AATCCATACCCACAAAAGCAGGCC .&%','(@''?7//+&)+2.+)0) +1378_161_317 141 * 0 0 * * 0 0 TTGGCCGGCAACCCCGGTACCTAA 7<,<'@)@>.)2@/')'&(?/-<( +1378_177_735 77 * 0 0 * * 0 0 CGAGCCCTAAACCATGAGATCGGA @@B>@AC9@A<B8@=9>7@5)>,0 +1378_177_735 141 * 0 0 * * 0 0 AGTACGCCATGTATTTGCGACCAG =?@?C<88@=>:7>@55/.,416, +1378_181_1684 77 * 0 0 * * 0 0 TTTCTGTTGTGGTTTTGTTGGGGT $##'$%'##%##$%$#$$####$* +1378_181_1684 141 * 0 0 * * 0 0 CGACTCCCGCATTCACGGTCAAGT &*#,##$#&$*$$#$#$$$#%$## +1378_187_1407 77 * 0 0 * * 0 0 TTGGGTGAAATCTTGTCGAGTGGA ####&##$$###$#####%##%%) +1378_187_1407 141 * 0 0 * * 0 0 TGGCGTCCACTCGTGGGTCTATCG $#$'%#$%$%&$%#####$#$#%# +1378_203_721 77 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/. +1378_203_721 141 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2& +1378_206_2039 77 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05 +1378_206_2039 141 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out3.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out3.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,2 @@ +@SQ SN:PHIX174 LN:5386 +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/bwa_wrapper_out4.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out4.sam Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,3 @@ +@SQ SN:PHIX174 LN:5386 +081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 1a56a541f9f9 -r 14d54c9dbd59 test-data/fastq_conv_in1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_in1.fastq Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 1a56a541f9f9 -r 14d54c9dbd59 tools/next_gen_conversion/fastq_conversions.xml --- a/tools/next_gen_conversion/fastq_conversions.xml Tue Sep 15 14:26:20 2009 -0400 +++ b/tools/next_gen_conversion/fastq_conversions.xml Wed Sep 16 11:14:39 2009 -0400 @@ -52,7 +52,7 @@ <tests> <test> <param name="type" value="sol2std" /> - <param name="input" value="bwa_phiX_sanger.fastq" ftype="fastqsolexa" /> + <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" /> <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" /> </test> <test> diff -r 1a56a541f9f9 -r 14d54c9dbd59 tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Tue Sep 15 14:26:20 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Wed Sep 16 11:14:39 2009 -0400 @@ -3,8 +3,6 @@ """ Runs BWA on single-end or paired-end data. Produces a SAM file containing the mappings. - -usage: python bwa_wrapper.py reference_sequence indexing_algorithm(is_or_bwtsw) forward_fastq_file reverse_fastq_file(or_None) output alignment_type(single_or_paired) parameters(pre_set_or_full) file_type(solexa_or_solid) file_source(indexed_or_history) maxEditDist fracMissingAligns maxGapOpens maxGapExtens disallowLongDel disallowIndel seed maxEditDistSeed numThreads mismatchPenalty gapOpenPenalty gapExtensPenalty colorSpaceRev suboptAlign noIterSearch outputTopN maxInsertSize maxOccurPairing\nThe last eighteen need to all be specified, or all be None """ import optparse, os, sys, tempfile @@ -16,6 +14,7 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() + parser.add_option('', '--threads', dest='threads', help='The number of threads to use') parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index') parser.add_option('', '--fastq', dest='fastq', help='The (forward) fastq file to use for the mapping') parser.add_option('', '--rfastq', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data') @@ -32,7 +31,6 @@ parser.add_option('-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps') parser.add_option('-l', '--seed', dest='seed', help='Take the first specified subsequences') parser.add_option('-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed') - parser.add_option('-t', '--numThreads', dest='numThreads', help='Number of threads') parser.add_option('-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty') parser.add_option('-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty') parser.add_option('-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty') @@ -42,8 +40,9 @@ parser.add_option('', '--outputTopN', dest='outputTopN', help='Output top specified hits') parser.add_option('', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good') parser.add_option('', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings') + parser.add_option('', '--dbkey', dest='dbkey', help='') (options, args) = parser.parse_args() - + # index if necessary if options.fileSource == 'history': # make temp directory for placement of indices and copy reference file there @@ -65,46 +64,42 @@ else: indexing_cmds = '-a %s' % indexingAlg options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1]) - cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref) + cmd1 = 'cd %s; bwa index %s %s 2> /dev/null' % (tmp_dir, indexing_cmds, options.ref) try: os.system(cmd1) except Exception, erf: stop_err('Error indexing reference sequence\n' + str(erf)) - # set up aligning and generate aligning command options if options.params == 'pre_set': if options.fileType == 'solid': - aligning_cmds = '-c' + aligning_cmds = '-c -t %s' % options.threads else: - aligning_cmds = '' + aligning_cmds = '-t %s' % options.threads gen_alignment_cmds = '' else: aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \ ((options.fracMissingAligns, options.maxEditDist)[options.maxEditDist != '0'], options.maxGapOpens, options.maxGapExtens, options.disallowLongDel, - options.disallowIndel, ('',' -l %s'%options.seed)[options.seed!=-1], - options.maxEditDistSeed, options.numThreads, options.mismatchPenalty, + options.disallowIndel, ('',' -l %s'%options.seed)[options.seed!='-1'], + options.maxEditDistSeed, options.threads, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty, ('',' -c')[options.colorSpaceRev=='true'], ('',' -R')[options.suboptAlign=='true'], ('',' -N')[options.noIterSearch=='true']) if options.genAlignType == 'single': gen_alignment_cmds = '-n %s' % options.outputTopN elif options.genAlignType == 'paired': gen_alignment_cmds = '-a %s -o %s' % (options.maxInsertSize, options.maxOccurPairing) - - # set up output file - file(options.output,'w').write('QNAME\tFLAG\tRNAME\tPOS\tMAPQ\tCIGAR\tMRNM\tMPOS\tISIZE\tSEQ\tQUAL\tOPT\n') + # set up output files tmp_align_out = tempfile.NamedTemporaryFile() + tmp_align_out2 = tempfile.NamedTemporaryFile() # prepare actual aligning and generate aligning commands cmd2 = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.fastq, tmp_align_out.name) cmd2b = '' if options.genAlignType == 'paired': - tmp_align_out2 = tempfile.NamedTemporaryFile() cmd2b = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.rfastq, tmp_align_out2.name) cmd3 = 'bwa sampe %s %s %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, tmp_align_out2.name, options.fastq, options.rfastq, options.output) else: cmd3 = 'bwa samse %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, options.fastq, options.output) - # align try: os.system(cmd2) @@ -116,11 +111,13 @@ os.system(cmd2b) except Exception, erf: stop_err("Error aligning second sequence\n" + str(erf)) - # generate align try: os.system(cmd3) except Exception, erf: stop_err("Error sequence aligning sequence\n" + str(erf)) - + # clean up temp files + tmp_align_out.close() + tmp_align_out2.close() + if __name__=="__main__": __main__() diff -r 1a56a541f9f9 -r 14d54c9dbd59 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Tue Sep 15 14:26:20 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Wed Sep 16 11:14:39 2009 -0400 @@ -1,7 +1,8 @@ -<tool id="bwa_wrapper" name="BWA" version="1.0.0"> +<tool id="bwa_wrapper" name="BWA" version="1.0.1"> <description> fast mapping of reads against reference sequence</description> <command interpreter="python"> bwa_wrapper.py + --threads="8" #if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history": --ref=$solidOrSolexa.solidRefGenomeSource.ownFile #else: @@ -27,7 +28,6 @@ --disallowIndel="None" --seed="None" --maxEditDistSeed="None" - --numThreads="None" --mismatchPenalty="None" --gapOpenPenalty="None" --gapExtensPenalty="None" @@ -46,7 +46,6 @@ --disallowIndel=$params.disallowIndel --seed=$params.seed --maxEditDistSeed=$params.maxEditDistSeed - --numThreads=$params.numThreads --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty @@ -57,9 +56,14 @@ --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing #end if + #if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history": + --dbkey=$dbkey + #else: + --dbkey="None" + #end if </command> <inputs> - <conditional name="solidOrSolexa"> + <conditional name="solidOrSolexa"> <param name="solidSolexa" type="select" label="Select SOLiD or Solexa format for the original dataset"> <option value="solexa">Solexa</option> <option value="solid">SOLiD</option> @@ -70,18 +74,18 @@ <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> - <when value="history"> - <param name="ownFile" type="data" format="fasta" label="Select a reference genome" /> - </when> <when value="indexed"> <param name="indices" type="select" label="Select a reference genome"> <options from_file="sequence_index_color.loc"> <column name="value" index="1" /> <column name="name" index="0" /> - <filter type="sort_by" column="0" /> + <filter type="sort_by" column="0" /> </options> </param> </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + </when> </conditional> </when> <when value="solexa"> @@ -90,39 +94,39 @@ <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> - <when value="history"> - <param name="ownFile" type="data" format="fasta" label="Select a reference genome" /> - </when> <when value="indexed"> <param name="indices" type="select" label="Select a reference genome"> <options from_file="sequence_index_base.loc"> <column name="value" index="1" /> <column name="name" index="0" /> - <filter type="sort_by" column="0" /> + <filter type="sort_by" column="0" /> </options> </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> </when> </conditional> </when> </conditional> - <conditional name="paired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" /> - </when> - <when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> - </when> - </conditional> - <conditional name="params"> + <conditional name="paired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input1" type="data" format="fastqsanger" label="FASTQ file" /> + </when> + <when value="paired"> + <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> + <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> + </when> + </conditional> + <conditional name="params"> <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List"> - <option value="pre_set">Commonly used</option> - <option value="full">Full Parameter List</option> - </param> + <option value="pre_set">Commonly used</option> + <option value="full">Full Parameter List</option> + </param> <when value="pre_set" /> <when value="full"> <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance" help="Enter this value OR a fraction of missing alignments, not both" /> @@ -133,9 +137,8 @@ <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end" /> <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed" help="Enter -1 for infinity" /> <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed" /> - <param name="numThreads" type="integer" value="1" label="Number of threads, in multi-threading mode" /> <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty" help="BWA will not search for suboptimal hits with a score lower than [value]" /> - <param name="gapOpenPenalty" type="integer" value="1" label="Gap open penalty" /> + <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty" /> <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty" /> <param name="colorSpaceRev" type="select" label="Reverse query but don't compement it" help="Reverse query for all alignment in color space"> <option value="false">Don't reverse query</option> @@ -150,34 +153,33 @@ </conditional> </inputs> <outputs> - <data format="tabular" name="output" /> + <data format="sam" name="output" /> </outputs> - - <help> + <help> **What it does** @@ -294,7 +291,7 @@ **Input formats** -BWA accepts files in FASTQ format. +BWA accepts files in Sanger FASTQ format. ------ @@ -336,7 +333,7 @@ ------- -**BWA Settings** +**BWA settings** All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here. @@ -390,9 +387,9 @@ -o INT Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing. [100000] - - </help> + </help> + <code file="bwa_wrapper_code.py" /> </tool> diff -r 1a56a541f9f9 -r 14d54c9dbd59 tools/sr_mapping/bwa_wrapper_code.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/sr_mapping/bwa_wrapper_code.py Wed Sep 16 11:14:39 2009 -0400 @@ -0,0 +1,8 @@ +import os + +def exec_before_job(app, inp_data, out_data, param_dict, tool): + try: + refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + except Exception, eq: + out_data['output'].set_dbkey(param_dict['dbkey'])

1 0

[hg] galaxy 2696: More fixes for cleanup_datasets.py
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bd160d40ee15 changeset: 2696:bd160d40ee15 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Sep 15 12:57:17 2009 -0400 description: More fixes for cleanup_datasets.py 1 file(s) affected in this change: scripts/cleanup_datasets/cleanup_datasets.py diffs (19 lines): diff -r b25489f4fb26 -r bd160d40ee15 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Tue Sep 15 12:04:14 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Tue Sep 15 12:57:17 2009 -0400 @@ -1,4 +1,6 @@ #!/usr/bin/env python + +import os, sys new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path @@ -8,7 +10,7 @@ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) -import sys, os, time, ConfigParser, shutil +import time, ConfigParser, shutil from datetime import datetime, timedelta from time import strftime from optparse import OptionParser

1 0

[hg] galaxy 2697: In Bowtie wrapper tool, removed --quiet option...
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1a56a541f9f9 changeset: 2697:1a56a541f9f9 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Sep 15 14:26:20 2009 -0400 description: In Bowtie wrapper tool, removed --quiet option and redirected stderr to /dev/null 1 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.py diffs (67 lines): diff -r bd160d40ee15 -r 1a56a541f9f9 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Tue Sep 15 12:57:17 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Tue Sep 15 14:26:20 2009 -0400 @@ -69,10 +69,10 @@ if options.genomeSource == 'history': # set up commands if options.index_settings =='index_pre_set': - indexing_cmds = '--quiet' + indexing_cmds = '' else: try: - indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s --quiet' % \ + indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ (('','--noauto')[options.iauto_b=='set'], ('','--packed')[options.ipacked=='packed'], ('','--bmax %s'%options.ibmax)[options.ibmax!='None' and options.ibmax>=1], @@ -87,7 +87,7 @@ ('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0], ('','--oldpmap')[options.ioldpmap=='yes']) except ValueError: - indexing_cmds = '--quiet' + indexing_cmds = '' # make temp directory for placement of indices and copy reference file there tmp_dir = tempfile.gettempdir() @@ -96,7 +96,7 @@ except Exception, erf: stop_err('Error creating temp directory for indexing purposes\n' + str(erf)) options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1]) - cmd1 = 'cd %s; bowtie-build %s -f %s %s' % (tmp_dir, indexing_cmds, options.ref, options.ref) + cmd1 = 'cd %s; bowtie-build %s -f %s %s 2> /dev/null' % (tmp_dir, indexing_cmds, options.ref, options.ref) try: os.system(cmd1) except Exception, erf: @@ -105,11 +105,11 @@ # set up aligning and generate aligning command options # automatically set threads to 8 in both cases if options.params == 'pre_set': - aligning_cmds = '-p %s --quiet' % options.threads + aligning_cmds = '-p %s' % options.threads else: try: aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s -p %s --quiet' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s -p %s' % \ (('','-s %s'%options.skip)[options.skip!='None'], ('','-u %s'%options.alignLimit)[int(options.alignLimit)>0], ('','-5 %s'%options.trimH)[int(options.trimH)>=0], @@ -138,15 +138,15 @@ ('','--seed %s'%options.seed)[int(options.seed)>=0], options.threads) except ValueError: - aligning_cmds = '-p %s --quiet' % options.threads + aligning_cmds = '-p %s' % options.threads tmp_out = tempfile.NamedTemporaryFile() # prepare actual aligning commands if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) else: - cmd2 = 'bowtie %s %s %s > %s' % (aligning_cmds, options.ref, options.input1, tmp_out.name) + cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, tmp_out.name) # prepare command to convert bowtie output to sam and alternative cmd3 = 'bowtie2sam.pl %s > %s' % (tmp_out.name, options.output) cmd4 = 'cp %s %s' % (tmp_out.name, options.output)

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[hg] galaxy 2694: More modifications to fastx toolkit: added fas...
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/990231e77b88 changeset: 2694:990231e77b88 user: guru date: Tue Sep 15 11:28:50 2009 -0400 description: More modifications to fastx toolkit: added fastqsanger to input format list and changed the ascii offset param to select. 4 file(s) affected in this change: tools/fastx_toolkit/fasta_nucleotide_changer.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastq_quality_filter.xml tools/fastx_toolkit/fastx_quality_statistics.xml diffs (82 lines): diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fasta_nucleotide_changer.xml --- a/tools/fastx_toolkit/fasta_nucleotide_changer.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fasta_nucleotide_changer.xml Tue Sep 15 11:28:50 2009 -0400 @@ -10,21 +10,21 @@ </param> </inputs> +  <param name="input" value="fasta_nuc_changer1.fasta" /> <param name="mode" value="-r" /> <output name="output" file="fasta_nuc_change1.out" /> </test> <test> -  <param name="input" value="fasta_nuc_changer2.fasta" /> <param name="mode" value="-d" /> <output name="output" file="fasta_nuc_change2.out" /> </test> </tests> - + --> <outputs> <data format="input" name="output" metadata_source="input" /> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastq_quality_converter.xml --- a/tools/fastx_toolkit/fastq_quality_converter.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Tue Sep 15 11:28:50 2009 -0400 @@ -2,15 +2,18 @@ <description>(ASCII-Numeric)</description> <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to convert" /> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to convert" /> <param name="QUAL_FORMAT" type="select" label="Desired output format"> <option value="-a">ASCII (letters) quality scores</option> <option value="-n">Numeric quality scores</option> </param> - <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> - </inputs> + <param name="offset" type="select" label="FASTQ ASCII offset"> + <option value="33">33</option> + <option value="64">64</option> + </param> + </inputs> <tests> <test> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastq_quality_filter.xml --- a/tools/fastx_toolkit/fastq_quality_filter.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_filter.xml Tue Sep 15 11:28:50 2009 -0400 @@ -4,7 +4,7 @@ <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command> <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to filter" /> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" /> <param name="quality" size="4" type="integer" value="20"> <label>Quality cut-off value</label> diff -r b179523d7d78 -r 990231e77b88 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Tue Sep 15 10:30:54 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Tue Sep 15 11:28:50 2009 -0400 @@ -3,8 +3,11 @@ <command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command> <inputs> - <param format="fasta,fastqsolexa" name="input" type="data" label="Library to analyse" /> - <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> + <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to analyse" /> + <param name="offset" type="select" label="FASTQ ASCII offset"> + <option value="33">33</option> + <option value="64">64</option> + </param> </inputs> <tests>

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[hg] galaxy 2693: Modification for input datatype in the splitter:w
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b179523d7d78 changeset: 2693:b179523d7d78 user: anton(a)nekrut-mbp.bx.psu.edu date: Tue Sep 15 10:30:54 2009 -0400 description: Modification for input datatype in the splitter:w 1 file(s) affected in this change: tools/metag_tools/split_paired_reads.xml diffs (21 lines): diff -r ba884f1a6b81 -r b179523d7d78 tools/metag_tools/split_paired_reads.xml --- a/tools/metag_tools/split_paired_reads.xml Tue Sep 15 10:15:42 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.xml Tue Sep 15 10:30:54 2009 -0400 @@ -4,7 +4,7 @@ split_paired_reads.py $input $output1 $output2 </command> <inputs> - <param name="input" type="data" format="fastqsolexa" label="Your paired-end file" /> + <param name="input" type="data" format="fastqsolexa,fastqsanger" label="Your paired-end file" /> </inputs> <outputs> <data name="output1" format="fastqsolexa"/> @@ -20,7 +20,7 @@ **What it does** -Splits a single fastq datasret representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length. +Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length. -----

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[hg] galaxy 2695: Add a new tool, Mutate by SNP codon, which wil...
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b25489f4fb26 changeset: 2695:b25489f4fb26 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 15 12:04:14 2009 -0400 description: Add a new tool, Mutate by SNP codon, which will take codon position and sequence information that is joined to SNP data and create a 'mutated codon'. 6 file(s) affected in this change: test-data/mutate_snp_codon_in.interval test-data/mutate_snp_codon_out.interval tool_conf.xml.main tool_conf.xml.sample tools/evolution/mutate_snp_codon.py tools/evolution/mutate_snp_codon.xml diffs (193 lines): diff -r 990231e77b88 -r b25489f4fb26 test-data/mutate_snp_codon_in.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutate_snp_codon_in.interval Tue Sep 15 12:04:14 2009 -0400 @@ -0,0 +1,6 @@ +chr1 58995 58998 NM_001005484 0 + GAA GAA Glu GAA 1177632 28.96 0 2787607 0.422452662804 585 chr1 58996 58997 rs1638318 0 + A A A/G genomic single by-submitter 0 0 unknown exact 3 +chr1 59289 59292 NM_001005484 0 + TTT TTT Phe TTT 714298 17.57 0 1538990 0.464134269878 585 chr1 59290 59291 rs71245814 0 + T T G/T genomic single unknown 0 0 unknown exact 3 +chr1 59313 59316 NM_001005484 0 + AAG AAG Lys AAG 1295568 31.86 0 2289189 0.565950648898 585 chr1 59315 59316 rs2854682 0 - G G C/T genomic single by-submitter 0 0 unknown exact 3 +chr1 59373 59376 NM_001005484 0 + ACA ACA Thr ACA 614523 15.11 0 2162384 0.284187729839 585 chr1 59373 59374 rs2691305 0 - A A C/T genomic single unknown 0 0 unknown exact 3 +chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs2531266 0 + G G C/G genomic single by-submitter 0 0 unknown exact 3 +chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs55874132 0 + G G C/G genomic single unknown 0 0 coding-synon exact 1 diff -r 990231e77b88 -r b25489f4fb26 test-data/mutate_snp_codon_out.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutate_snp_codon_out.interval Tue Sep 15 12:04:14 2009 -0400 @@ -0,0 +1,6 @@ +chr1 58995 58998 NM_001005484 0 + GAA GAA Glu GAA 1177632 28.96 0 2787607 0.422452662804 585 chr1 58996 58997 rs1638318 0 + A A A/G genomic single by-submitter 0 0 unknown exact 3 GGA +chr1 59289 59292 NM_001005484 0 + TTT TTT Phe TTT 714298 17.57 0 1538990 0.464134269878 585 chr1 59290 59291 rs71245814 0 + T T G/T genomic single unknown 0 0 unknown exact 3 TGT +chr1 59313 59316 NM_001005484 0 + AAG AAG Lys AAG 1295568 31.86 0 2289189 0.565950648898 585 chr1 59315 59316 rs2854682 0 - G G C/T genomic single by-submitter 0 0 unknown exact 3 AAA +chr1 59373 59376 NM_001005484 0 + ACA ACA Thr ACA 614523 15.11 0 2162384 0.284187729839 585 chr1 59373 59374 rs2691305 0 - A A C/T genomic single unknown 0 0 unknown exact 3 GCA +chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs2531266 0 + G G C/G genomic single by-submitter 0 0 unknown exact 3 GCC +chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs55874132 0 + G G C/G genomic single unknown 0 0 coding-synon exact 1 GCC diff -r 990231e77b88 -r b25489f4fb26 tool_conf.xml.main --- a/tool_conf.xml.main Tue Sep 15 11:28:50 2009 -0400 +++ b/tool_conf.xml.main Tue Sep 15 12:04:14 2009 -0400 @@ -132,10 +132,11 @@ <tool file="regVariation/best_regression_subsets.xml" /> <tool file="regVariation/rcve.xml" /> </section> - <section name="Evolution: HyPhy" id="hyphy"> + <section name="Evolution" id="hyphy"> <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> <tool file="hyphy/hyphy_dnds_wrapper.xml" /> + <tool file="evolution/mutate_snp_codon.xml" /> </section> <section name="Metagenomic analyses" id="tax_manipulation"> <tool file="taxonomy/gi2taxonomy.xml" /> diff -r 990231e77b88 -r b25489f4fb26 tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Sep 15 11:28:50 2009 -0400 +++ b/tool_conf.xml.sample Tue Sep 15 12:04:14 2009 -0400 @@ -152,10 +152,11 @@ <tool file="regVariation/best_regression_subsets.xml" /> <tool file="regVariation/rcve.xml" /> </section> - <section name="Evolution: HyPhy" id="hyphy"> + <section name="Evolution" id="hyphy"> <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> <tool file="hyphy/hyphy_dnds_wrapper.xml" /> + <tool file="evolution/mutate_snp_codon.xml" /> </section> <section name="Metagenomic analyses" id="tax_manipulation"> <tool file="taxonomy/gi2taxonomy.xml" /> diff -r 990231e77b88 -r b25489f4fb26 tools/evolution/mutate_snp_codon.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/mutate_snp_codon.py Tue Sep 15 12:04:14 2009 -0400 @@ -0,0 +1,73 @@ +#!/usr/bin/env python +""" +Script to mutate SNP codons. +Dan Blankenberg +""" + +import sys, string + +def strandify( fields, column ): + strand = '+' + if column >= 0 and column < len( fields ): + strand = fields[ column ] + if strand not in [ '+', '-' ]: + strand = '+' + return strand + +def main(): + # parse command line + input_file = sys.argv[1] + out = open( sys.argv[2], 'wb+' ) + codon_chrom_col = int( sys.argv[3] ) - 1 + codon_start_col = int( sys.argv[4] ) - 1 + codon_end_col = int( sys.argv[5] ) - 1 + codon_strand_col = int( sys.argv[6] ) - 1 + codon_seq_col = int( sys.argv[7] ) - 1 + + snp_chrom_col = int( sys.argv[8] ) - 1 + snp_start_col = int( sys.argv[9] ) - 1 + snp_end_col = int( sys.argv[10] ) - 1 + snp_strand_col = int( sys.argv[11] ) - 1 + snp_observed_col = int( sys.argv[12] ) - 1 + + max_field_index = max( codon_chrom_col, codon_start_col, codon_end_col, codon_strand_col, codon_seq_col, snp_chrom_col, snp_start_col, snp_end_col, snp_strand_col, snp_observed_col ) + + DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" ) + skipped_lines = 0 + for line in open( input_file ): + line = line.rstrip( '\n\r' ) + if line and not line.startswith( '#' ): + fields = line.split( '\t' ) + if max_field_index >= len( fields ): + skipped_lines += 1 + continue + codon_chrom = fields[codon_chrom_col] + codon_start = int( fields[codon_start_col] ) + codon_end = int( fields[codon_end_col] ) + codon_strand = strandify( fields, codon_strand_col ) + codon_seq = fields[codon_seq_col].upper() + + snp_chrom = fields[snp_chrom_col] + snp_start = int( fields[snp_start_col] ) + snp_end = int( fields[snp_end_col] ) + snp_strand = strandify( fields, snp_strand_col ) + snp_observed = fields[snp_observed_col].split( '/' ) + + for observed in snp_observed: + #Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2 + offset = snp_start - codon_start + if codon_strand == '-': + offset = 2 - offset + assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset ) + + if codon_strand != snp_strand: + #if our SNP is on a different strand than our codon, take complement of provided observed SNP base + observed = observed.translate( DNA_COMP ) + snp_codon = [ char for char in codon_seq ] + snp_codon[offset] = observed.upper() + snp_codon = ''.join( snp_codon ) + + if codon_seq != snp_codon: #only output when we actually have a different codon + out.write( "%s\t%s\n" % ( line, snp_codon ) ) + +if __name__ == "__main__": main() diff -r 990231e77b88 -r b25489f4fb26 tools/evolution/mutate_snp_codon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/mutate_snp_codon.xml Tue Sep 15 12:04:14 2009 -0400 @@ -0,0 +1,60 @@ +<tool id="mutate_snp_codon_1" name="Mutate Codons" version="1.0.0"> + <description>with SNPs</description> + <command interpreter="python">mutate_snp_codon.py $input1 $output1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $codon_seq_col $snp_chrom_col $snp_start_col $snp_end_col $snp_strand_col $snp_observed_col</command> + <inputs> + <param name="input1" type="data" format="interval" label="Interval file with joined SNPs" optional="False" help="The interval metadata for this file should be set for the codon positions."/> + <param name="codon_seq_col" label="Codon Sequence column" type="data_column" data_ref="input1" /> + <param name="snp_chrom_col" label="SNP chromosome column" type="data_column" data_ref="input1" /> + <param name="snp_start_col" label="SNP start column" type="data_column" data_ref="input1" /> + <param name="snp_end_col" label="SNP end column" type="data_column" data_ref="input1" /> + <param name="snp_strand_col" label="SNP strand column" type="data_column" data_ref="input1" /> + <param name="snp_observed_col" label="SNP observed column" type="data_column" data_ref="input1" /> + </inputs> + <outputs> + <data name="output1" format="interval" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="mutate_snp_codon_in.interval"/> + <param name="codon_seq_col" value="8"/> + <param name="snp_chrom_col" value="17"/> + <param name="snp_start_col" value="18"/> + <param name="snp_end_col" value="19"/> + <param name="snp_strand_col" value="22"/> + <param name="snp_observed_col" value="25"/> + <output name="output1" file="mutate_snp_codon_out.interval" /> + </test> + </tests> + <help> +This tool takes an interval file as input. This input should contain a set of codon locations and corresponding DNA sequence (such as from the *Extract Genomic DNA* tool) joined to SNP locations with observed values (such as *all fields from selected table* from the snp130 table of hg18 at the UCSC Table browser). This interval file should have the metadata (chromosome, start, end, strand) set for the columns containing the locations of the codons. The user needs to specify the columns containing the sequence for the codon as well as the genomic positions and observed values (values should be split by '/') for the SNP data as tool input; SNPs positions and sequence substitutes must have a length of exactly 1. Only genomic intervals which yield a different sequence string are output. All sequence characters are converted to uppercase during processing. + + For example, using these settings: + + * **metadata** **chromosome**, **start**, **end** and **strand** set to **1**, **2**, **3** and **6**, respectively + * **Codon Sequence column** set to **c8** + * **SNP chromosome column** set to **c17** + * **SNP start column** set to **c18** + * **SNP end column** set to **c19** + * **SNP strand column** set to **c22** + * **SNP observed column** set to **c25** + + with the following input:: + + chr1 58995 58998 NM_001005484 0 + GAA GAA Glu GAA 1177632 28.96 0 2787607 0.422452662804 585 chr1 58996 58997 rs1638318 0 + A A A/G genomic single by-submitter 0 0 unknown exact 3 + chr1 59289 59292 NM_001005484 0 + TTT TTT Phe TTT 714298 17.57 0 1538990 0.464134269878 585 chr1 59290 59291 rs71245814 0 + T T G/T genomic single unknown 0 0 unknown exact 3 + chr1 59313 59316 NM_001005484 0 + AAG AAG Lys AAG 1295568 31.86 0 2289189 0.565950648898 585 chr1 59315 59316 rs2854682 0 - G G C/T genomic single by-submitter 0 0 unknown exact 3 + chr1 59373 59376 NM_001005484 0 + ACA ACA Thr ACA 614523 15.11 0 2162384 0.284187729839 585 chr1 59373 59374 rs2691305 0 - A A C/T genomic single unknown 0 0 unknown exact 3 + chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs2531266 0 + G G C/G genomic single by-submitter 0 0 unknown exact 3 + chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs55874132 0 + G G C/G genomic single unknown 0 0 coding-synon exact 1 + + + will produce:: + + chr1 58995 58998 NM_001005484 0 + GAA GAA Glu GAA 1177632 28.96 0 2787607 0.422452662804 585 chr1 58996 58997 rs1638318 0 + A A A/G genomic single by-submitter 0 0 unknown exact 3 GGA + chr1 59289 59292 NM_001005484 0 + TTT TTT Phe TTT 714298 17.57 0 1538990 0.464134269878 585 chr1 59290 59291 rs71245814 0 + T T G/T genomic single unknown 0 0 unknown exact 3 TGT + chr1 59313 59316 NM_001005484 0 + AAG AAG Lys AAG 1295568 31.86 0 2289189 0.565950648898 585 chr1 59315 59316 rs2854682 0 - G G C/T genomic single by-submitter 0 0 unknown exact 3 AAA + chr1 59373 59376 NM_001005484 0 + ACA ACA Thr ACA 614523 15.11 0 2162384 0.284187729839 585 chr1 59373 59374 rs2691305 0 - A A C/T genomic single unknown 0 0 unknown exact 3 GCA + chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs2531266 0 + G G C/G genomic single by-submitter 0 0 unknown exact 3 GCC + chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs55874132 0 + G G C/G genomic single unknown 0 0 coding-synon exact 1 GCC + </help> +</tool>

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[hg] galaxy 2691: Updating FASTX tool-set to the latest version ...
by Nate Coraor 16 Sep '09

16 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/40c5e1853a66 changeset: 2691:40c5e1853a66 user: gua110 date: Mon Sep 14 17:03:17 2009 -0400 description: Updating FASTX tool-set to the latest version v0.0.10 28 file(s) affected in this change: static/fastx_icons/fasta_clipping_histogram_3.png static/fastx_icons/fasta_clipping_histogram_4.png test-data/fasta_collapser1.out test-data/fasta_formatter1.fasta test-data/fasta_formatter1.out test-data/fasta_formatter2.out test-data/fasta_nuc_changer1.fasta test-data/fasta_nuc_changer1.out test-data/fasta_nuc_changer2.fasta test-data/fasta_nuc_changer2.out test-data/fastq_stats1.out tool-data/fastx_clipper_sequences.txt tool_conf.xml.sample tools/fastx_toolkit/fasta_clipping_histogram.xml tools/fastx_toolkit/fasta_collapser.xml tools/fastx_toolkit/fasta_formatter.xml tools/fastx_toolkit/fasta_nucleotide_changer.xml tools/fastx_toolkit/fastq_nucleotides_distribution.xml tools/fastx_toolkit/fastq_qual_conv.xml tools/fastx_toolkit/fastq_qual_stat.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastx_barcode_splitter.xml tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh tools/fastx_toolkit/fastx_clipper.xml tools/fastx_toolkit/fastx_collapser.xml tools/fastx_toolkit/fastx_nucleotides_distribution.xml tools/fastx_toolkit/fastx_quality_statistics.xml tools/fastx_toolkit/fastx_renamer.xml diffs (1772 lines): diff -r 0f97b3048bc3 -r 40c5e1853a66 static/fastx_icons/fasta_clipping_histogram_3.png Binary file static/fastx_icons/fasta_clipping_histogram_3.png has changed diff -r 0f97b3048bc3 -r 40c5e1853a66 static/fastx_icons/fasta_clipping_histogram_4.png Binary file static/fastx_icons/fasta_clipping_histogram_4.png has changed diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_collapser1.out --- a/test-data/fasta_collapser1.out Mon Sep 14 15:27:55 2009 -0400 +++ b/test-data/fasta_collapser1.out Mon Sep 14 17:03:17 2009 -0400 @@ -1,24 +1,24 @@ ->1-3 +>1-15 +AGTACAAGGACATGC +>2-11 +ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>3-5 +TTCAACGCCGCCGTGAAC +>4-3 CTGCTGCGATCGGTGTGC ->2-1 -TTACCTCACGATATTGTAATA ->3-1 -CCTTGTAGTGGATTCTGATGA ->4-1 -TGATTTCCAGAGCCAAT ->5-11 -ATTGCTGCTCGGATGGTCCGGCTGTGCACAC +>5-1 +TCAAATTCTAGATTTTTACGG >6-1 ACCATTCGAGCATAC >7-1 +TGATTTCCAGAGCCAAT +>8-1 +TTACCTCACGATATTGTAATA +>9-1 +TGTATTTACAATGACTAGAAA +>10-1 +CCTTGTAGTGGATTCTGATGA +>11-1 CGATTGCCGAAGTCTACCA ->8-5 -TTCAACGCCGCCGTGAAC ->9-1 -ATGACTTCATCGTCCACCCTTTAGAACT ->10-15 -AGTACAAGGACATGC ->11-1 -TCAAATTCTAGATTTTTACGG >12-1 -TGTATTTACAATGACTAGAAA +ATGACTTCATCGTCCACCCTTTAGAACT \ No newline at end of file diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_formatter1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_formatter1.fasta Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,100 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC +CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG +TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA +GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT +ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC +TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC +AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT +GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA +GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG +AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT +AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA +AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG +AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA +ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC +GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA +CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA +ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG +TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG +GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa +ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag +ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga +taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt +ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca +ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct +tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat +aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG +TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC +CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA +AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA +AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT +GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA +ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT +AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT +ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT +GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA +CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG +ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA +TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT +TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT +AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT +TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC +GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC +GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT +ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG +TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA +TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA +TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaatttt +ttggataatttttttttggataaatagttcttttttgataattctaataa +tttttttatttattttttttttttctataattttttttaaaaaatttatt +aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC +AATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC +GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT +TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA +TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg +tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG +ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt +gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT +GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA +AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA +CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG +AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA +GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact +atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca +tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga +aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt +tagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA +GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT +ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat +atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc +tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT +TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctct +ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG +TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT +AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA +CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA +CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT +CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG +GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA +TTA diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_formatter1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_formatter1.out Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,10 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATA TGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATAT GATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_formatter2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_formatter2.out Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,84 @@ +>Scaffold3648 +AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA +GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG +TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA +ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA +CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT +TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA +AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT +CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG +CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC +CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT +TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC +ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA +AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC +ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC +TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT +ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT +TCGATATAGTACATGGACACAATTAAATATGATATTGTCT +>Scaffold9299 +CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA +TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT +TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat +ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa +tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt +gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag +tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct +tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca +caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA +CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT +GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG +AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG +AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA +AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA +ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT +CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT +TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG +GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA +ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT +CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA +>Scaffold9309 +GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA +AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA +TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG +ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT +GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT +ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG +ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG +GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT +GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT +GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt +gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt +tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt +ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA +ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA +>Scaffold9310 +GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA +GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA +TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg +tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt +ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA +ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt +gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT +GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG +AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA +GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA +AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC +AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa +aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc +ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc +aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA +>Scaffold11911 +TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT +TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT +GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt +gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG +TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT +TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct +ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT +GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT +TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT +ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA +GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT +AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC +TTTGATGCCAATCCAACAATTTTGCATATATTA diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_nuc_changer1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_nuc_changer1.fasta Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_nuc_changer1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_nuc_changer1.out Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_nuc_changer2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_nuc_changer2.fasta Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +UGAGGUAGUAGGUUGUAUAGUU +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +UCCCUGAGACCUCAAGUGUGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +UGGAAUGUAAAGAAGUAUGUA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +UAUCACAGCCAGCUUUGAUGUGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGUGUGGUUAGCUGGUUG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +UCACCGGGUGGAAACUAGCAGU +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +UCACCGGGUGAAAAUUCGCAUG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +UCACCGGGUGAACACUUGCAGU +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +UCACCGGGAGAAAAACUGGAGU +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +UCACCGGGUGUAAAUCAGCUUG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +UCACCGGGUGUACAUCAGCUAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +UCACCGGGUGAAAAAUCACCUA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +UCACCGGGUUAACAUCUACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +UAUCACAGUUUACUUGCUGUCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +UGACUAGAGACACAUUCAGCU +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +UGACUAGAGACACAUUCAGCU +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +UGUCAUGGAGUCGCUCUCUUCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +UGUCAUGGAGGCGCUCUCUUCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +UGAGGUAGGCUCAGUAGAUGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCUGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +UGAUAUGUCUGGUAUUCUUGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +UACCCGUAGCUCCUAUCCAUGUU +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGUACAUAUGUUUCCGUGCU +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGUACAUUUGUUUCCGUGCU +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +UACCCGUAAUCUUCAUAAUCCGAG diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fasta_nuc_changer2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_nuc_changer2.out Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,50 @@ +>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 +TGAGGTAGTAGGTTGTATAGTT +>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 +TCCCTGAGACCTCAAGTGTGA +>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 +TGGAATGTAAAGAAGTATGTA +>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2 +TATCACAGCCAGCTTTGATGTGC +>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34 +AGGCAGTGTGGTTAGCTGGTTG +>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35 +TCACCGGGTGGAAACTAGCAGT +>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42 +TCACCGGGTTAACATCTACAGA +>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43 +TATCACAGTTTACTTGCTGTCGC +>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44 +TGACTAGAGACACATTCAGCT +>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45 +TGACTAGAGACACATTCAGCT +>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46 +TGTCATGGAGTCGCTCTCTTCA +>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47 +TGTCATGGAGGCGCTCTCTTCA +>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48 +TGAGGTAGGCTCAGTAGATGCGA +>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 +AAGCACCACGAGAAGCTGCAGA +>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 +TGATATGTCTGGTATTCTTGGG +>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51 +TACCCGTAGCTCCTATCCATGTT +>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52 +CACCCGTACATATGTTTCCGTGCT +>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53 +CACCCGTACATTTGTTTCCGTGCT +>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54 +TACCCGTAATCTTCATAATCCGAG diff -r 0f97b3048bc3 -r 40c5e1853a66 test-data/fastq_stats1.out --- a/test-data/fastq_stats1.out Mon Sep 14 15:27:55 2009 -0400 +++ b/test-data/fastq_stats1.out Mon Sep 14 17:03:17 2009 -0400 @@ -1,37 +1,37 @@ -column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count -1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 -2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 -3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 -4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 -5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 -6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 -7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 -8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 -9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 -10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 -11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 -12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 -13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 -14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 -15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 -16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 -17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 -18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 -19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 -20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 -21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 -22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 -23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 -24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 -25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 -26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 -27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 -28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 -29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 -30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 -31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 -32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 -33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 -34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 -35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 -36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 +22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 +23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 +24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 +25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 +26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 +27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 +28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 +29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 +30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 +31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 +32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 +33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 +34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 +35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 +36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 9 diff -r 0f97b3048bc3 -r 40c5e1853a66 tool-data/fastx_clipper_sequences.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fastx_clipper_sequences.txt Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,13 @@ +# +# Adapter/Linker sequences for FASTX-Clipper tool. +# +# Format: +# Adapter Sequence <TAB> Descriptive name +# +# Example: +# AAATTTGATAAGATA Our-Adapter +# +# Some adapters can be found here: +# http://seqanswers.com/forums/showthread.php?t=198 + +TGTAGGCC Dummy-Adapter (don't use me) diff -r 0f97b3048bc3 -r 40c5e1853a66 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Sep 14 15:27:55 2009 -0400 +++ b/tool_conf.xml.sample Mon Sep 14 17:03:17 2009 -0400 @@ -299,24 +299,26 @@ <tool file="fasta_tools/tabular_to_fasta.xml" /> </section> <section name="FASTA/Q Information" id="cshl_library_information"> - <tool file="fastx_toolkit/fastq_qual_stat.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastq_nucleotides_distribution.xml" /> -  + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="fastx_toolkit/fasta_clipping_histogram.xml" /> </section> <section name="FASTA/Q Preprocessing" id="cshl_fastx_manipulation"> <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_qual_conv.xml" /> -  + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_clipper.xml" /> <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fasta_formatter.xml" /> + <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> <tool file="fastx_toolkit/fastq_quality_filter.xml" /> -  -  + <tool file="fastx_toolkit/fastx_collapser.xml" /> +  </section> - <section name="Short Read QC and Manipulation" id="short_read_analysis"> <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_figure_high_quality_length.xml" /> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fasta_clipping_histogram.xml --- a/tools/fastx_toolkit/fasta_clipping_histogram.xml Mon Sep 14 15:27:55 2009 -0400 +++ b/tools/fastx_toolkit/fasta_clipping_histogram.xml Mon Sep 14 17:03:17 2009 -0400 @@ -13,7 +13,7 @@ **What it does** -This tool creates a histogram image of sequence lengths distribution in a given fasta data set file. +This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file. **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results. @@ -21,17 +21,82 @@ **Output Examples** - In the following library, most sequences are 24-mers to 27-mers. This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ../static/fastx_icons/fasta_clipping_histogram_1.png +.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png In the following library, most sequences are 19,22 or 23-mers. This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ../static/fastx_icons/fasta_clipping_histogram_2.png +.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png + + +----- + + +**Input Formats** + +This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so:: + + >sequence1 + AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG + >sequence2 + GTGTGTGTGGGAAGTTGACACAGTA + >sequence3 + CCTTGAGATTAACGCTAATCAAGTAAAC + + +If the sequences span over multiple lines:: + + >sequence1 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG + +Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: + + >sequence1 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + + +----- + + + +**Multiplicity counts (a.k.a reads-count)** + +If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing). + +Example 1 - The following FASTA file *does not* have multiplicity counts:: + + >seq1 + GGATCC + >seq2 + GGTCATGGGTTTAAA + >seq3 + GGGATATATCCCCACACACACACAC + +Each sequence is counts as one, to produce the following chart: + +.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png + + +Example 2 - The following FASTA file have multiplicity counts:: + + >seq1-2 + GGATCC + >seq2-10 + GGTCATGGGTTTAAA + >seq3-3 + GGGATATATCCCCACACACACACAC + +The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: + +.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png + +Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. </help> </tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fasta_collapser.xml --- a/tools/fastx_toolkit/fasta_collapser.xml Mon Sep 14 15:27:55 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -<tool id="cshl_fasta_collapser" name="Collapse"> - <description>sequences</description> - <command>fasta_collapser.pl $input $output</command> - - <inputs> - <param format="fasta" name="input" type="data" label="Library to collapse" /> - </inputs> - - <tests> - <test> - <param name="input" value="fasta_collapser1.fasta" /> - <output name="output" file="fasta_collapser1.out" /> - </test> - </tests> - - <outputs> - <data format="fasta" name="output" metadata_source="input" /> - </outputs> - <help> - -**What it does** - -This tool collapses identical sequences in a FASTA file into a single sequence. - --------- - -**Example** - -Example Input File (Sequence "ATAT" appears multiple times):: - - >CSHL_2_FC0042AGLLOO_1_1_605_414 - TGCG - >CSHL_2_FC0042AGLLOO_1_1_537_759 - ATAT - >CSHL_2_FC0042AGLLOO_1_1_774_520 - TGGC - >CSHL_2_FC0042AGLLOO_1_1_742_502 - ATAT - >CSHL_2_FC0042AGLLOO_1_1_781_514 - TGAG - >CSHL_2_FC0042AGLLOO_1_1_757_487 - TTCA - >CSHL_2_FC0042AGLLOO_1_1_903_769 - ATAT - >CSHL_2_FC0042AGLLOO_1_1_724_499 - ATAT - -Example Output file:: - - >1-1 - TGCG - >2-4 - ATAT - >3-1 - TGGC - >4-1 - TGAG - >5-1 - TTCA - -.. class:: infomark - -Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. - -The output seqeunce name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. - -The following output:: - - >2-4 - ATAT - -means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. - -</help> -</tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fasta_formatter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fasta_formatter.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,79 @@ +<tool id="cshl_fasta_formatter" name="FASTA Width"> + <description>formatter</description> +  + <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command> + <inputs> + <param format="fasta" name="input" type="data" label="Library to re-format" /> + + <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line outout." /> + </inputs> + + <tests> + <test> +  + <param name="input" value="fasta_formatter1.fasta" /> + <param name="width" value="0" /> + <output name="output" file="fastx_formatter1.out" /> + </test> + <test> +  + <param name="input" value="fasta_formatter1.fasta" /> + <param name="width" value="60" /> + <output name="output" file="fasta_formatter2.out" /> + </test> + </tests> + + <outputs> + <data format="input" name="output" metadata_source="input" /> + </outputs> + +<help> +**What it does** + +This tool re-formats a FASTA file, changing the width of the nucleotides lines. + +**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. + +-------- + +**Example** + +Input FASTA file (each nucleotides line is 50 characters long):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC + CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG + TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA + ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG + TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG + aactggtctttacctTTAAGTTG + + +Output FASTA file (with width=80):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT + ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA + ATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC + GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG + +Output FASTA file (with width=0 => single line):: + + >Scaffold3648 + AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT + >Scaffold9299 + CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG +</help> +</tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fasta_nucleotide_changer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fasta_nucleotide_changer.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,65 @@ +<tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" > + <description>converter</description> + <command>zcat -f '$input' | fasta_nucleotide_changer $mode -v -o $output</command> + <inputs> + <param format="fasta" name="input" type="data" label="Library to convert" /> + + <param name="mode" type="select" label="Convert"> + <option value="-d">RNA to DNA (U to T)</option> + <option value="-r">DNA to RNA (T to U)</option> + </param> + </inputs> + + <tests> + <test> +  + <param name="input" value="fasta_nuc_changer1.fasta" /> + <param name="mode" value="-r" /> + <output name="output" file="fasta_nuc_change1.out" /> + </test> + <test> +  + <param name="input" value="fasta_nuc_changer2.fasta" /> + <param name="mode" value="-d" /> + <output name="output" file="fasta_nuc_change2.out" /> + </test> + </tests> + + + <outputs> + <data format="input" name="output" metadata_source="input" /> + </outputs> + +<help> +**What it does** + +This tool converts RNA FASTA files to DNA (and vice-versa). + +In **RNA-to-DNA** mode, U's are changed into T's. + +In **DNA-to-RNA** mode, T's are changed into U's. + +-------- + +**Example** + +Input RNA FASTA file ( from Sanger's mirBase ):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + UGAGGUAGUAGGUUGUAUAGUU + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + UCCCUGAGACCUCAAGUGUGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + UGGAAUGUAAAGAAGUAUGUA + +Output DNA FASTA file (with RNA-to-DNA mode):: + + >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 + TGAGGTAGTAGGTTGTATAGTT + >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 + TCCCTGAGACCTCAAGTGTGA + >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 + TGGAATGTAAAGAAGTATGTA + +</help> +</tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastq_nucleotides_distribution.xml --- a/tools/fastx_toolkit/fastq_nucleotides_distribution.xml Mon Sep 14 15:27:55 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="cshl_fastq_nucleotides_distribution" name="Nucleotides Distribution"> - <description>chart</description> - <command>fastq_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command> - - <inputs> - <param format="txt" name="input" type="data" label="Statistics Text File (output of 'FASTQ Statistics' tool)" /> - </inputs> - - <outputs> - <data format="png" name="output" metadata_source="input" /> - </outputs> -<help> - -**What it does** - -Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. - -.. class:: infomark - -**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. - ------ - -**Output Examples** - - - -The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** - -.. image:: ../static/fastx_icons/fastq_nucleotides_distribution_1.png - - - - - - - -In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** - -.. image:: ../static/fastx_icons/fastq_nucleotides_distribution_2.png - - - - - - - - -The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): - -.. image:: ../static/fastx_icons/fastq_nucleotides_distribution_3.png - - - - - - - - -But most of the time, the chart will look rather random: - -.. image:: ../static/fastx_icons/fastq_nucleotides_distribution_4.png - -</help> -</tool> - diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastq_qual_conv.xml --- a/tools/fastx_toolkit/fastq_qual_conv.xml Mon Sep 14 15:27:55 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -<tool id="cshl_fastq_qual_conv" name="Quality format converter"> - <description>(ASCII-Numeric)</description> - <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output</command> - <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to convert" /> - - <param name="QUAL_FORMAT" type="select" label="Desired output format"> - <option value="-a">ASCII (letters) quality scores</option> - <option value="-n">Numeric quality scores</option> - </param> - </inputs> - - <tests> - <test> -  - <param name="input" value="fastq_qual_conv1.fastq" /> - <param name="QUAL_FORMAT" value="Numeric quality scores" /> - <output name="output" file="fastq_qual_conv1.out" /> - </test> - <test> -  - <param name="input" value="fastq_qual_conv1.fastq" /> - <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> - <output name="output" file="fastq_qual_conv1a.out" /> - </test> - <test> -  - <param name="input" value="fastq_qual_conv2.fastq" /> - <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> - <output name="output" file="fastq_qual_conv2.out" /> - </test> - <test> -  - <param name="input" value="fastq_qual_conv2.fastq" /> - <param name="QUAL_FORMAT" value="Numeric quality scores" /> - <output name="output" file="fastq_qual_conv2n.out" /> - </test> - </tests> - - <outputs> - <data format="fastqsolexa" name="output" metadata_source="input" /> - </outputs> -<help> - -**What it does** - -Converts a solexa FASTQ file to/from numeric or ASCII quality format. - -.. class:: warningmark - -Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). - - ------ - -FASTQ with Numeric quality scores:: - - @CSHL__2_FC042AGWWWXX:8:1:120:202 - ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC - +CSHL__2_FC042AGWWWXX:8:1:120:202 - 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 - @CSHL__2_FC042AGWWWXX:8:1:103:1185 - ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC - +CSHL__2_FC042AGWWWXX:8:1:103:1185 - 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 - - -FASTQ with ASCII quality scores:: - - @CSHL__2_FC042AGWWWXX:8:1:120:202 - ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC - +CSHL__2_FC042AGWWWXX:8:1:120:202 - hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH - @CSHL__2_FC042AGWWWXX:8:1:103:1185 - ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC - +CSHL__2_FC042AGWWWXX:8:1:103:1185 - hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B - - -</help> -</tool> - diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastq_qual_stat.xml --- a/tools/fastx_toolkit/fastq_qual_stat.xml Mon Sep 14 15:27:55 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -<tool id="cshl_fastq_qual_stat" name="Quality Statistics"> - <description></description> - <command>zcat -f $input | fastq_quality_stats -o $output</command> - - <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to analyse" /> - </inputs> - - <tests> - <test> - <param name="input" value="fastq_stats1.fastq" /> - <output name="output" file="fastq_stats1.out" /> - </test> - </tests> - - <outputs> - <data format="txt" name="output" metadata_source="input" /> - </outputs> - -<help> - -**What it does** - -Creates quality statistics report for the given Solexa/FASTQ library. - -.. class:: infomark - -**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. - ------ - -**The output file will contain the following fields:** - -* column = column number (1 to 36 for a 36-cycles read solexa file) -* count = number of bases found in this column. -* min = Lowest quality score value found in this column. -* max = Highest quality score value found in this column. -* sum = Sum of quality score values for this column. -* mean = Mean quality score value for this column. -* Q1 = 1st quartile quality score. -* med = Median quality score. -* Q3 = 3rd quartile quality score. -* IQR = Inter-Quartile range (Q3-Q1). -* lW = 'Left-Whisker' value (for boxplotting). -* rW = 'Right-Whisker' value (for boxplotting). -* A_Count = Count of 'A' nucleotides found in this column. -* C_Count = Count of 'C' nucleotides found in this column. -* G_Count = Count of 'G' nucleotides found in this column. -* T_Count = Count of 'T' nucleotides found in this column. -* N_Count = Count of 'N' nucleotides found in this column. - - - - - - -**Output Example**:: - - column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count - 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 - 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 - 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 - 4 6362991 -5 40 247654797 38.92 40 40 40 0 40 40 1683197 1410855 1722633 1546306 0 - 5 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 - 6 6362991 -5 40 248499903 39.05 40 40 40 0 40 40 1598956 1236081 1568608 1959346 0 - 7 6362991 -4 40 247719760 38.93 40 40 40 0 40 40 1692667 1822140 1496741 1351443 0 - 8 6362991 -5 40 245745205 38.62 40 40 40 0 40 40 2230936 1343260 1529928 1258867 0 - 9 6362991 -5 40 245766735 38.62 40 40 40 0 40 40 1702064 1306257 1336511 2018159 0 - 10 6362991 -5 40 245089706 38.52 40 40 40 0 40 40 1519917 1446370 1450995 1945709 0 - 11 6362991 -5 40 242641359 38.13 40 40 40 0 40 40 1717434 1282975 1387804 1974778 0 - 12 6362991 -5 40 242026113 38.04 40 40 40 0 40 40 1662872 1202041 1519721 1978357 0 - 13 6362991 -5 40 238704245 37.51 40 40 40 0 40 40 1549965 1271411 1973291 1566681 1643 - 14 6362991 -5 40 235622401 37.03 40 40 40 0 40 40 2101301 1141451 1603990 1515774 475 - 15 6362991 -5 40 230766669 36.27 40 40 40 0 40 40 2344003 1058571 1440466 1519865 86 - 16 6362991 -5 40 224466237 35.28 38 40 40 2 35 40 2203515 1026017 1474060 1651582 7817 - 17 6362991 -5 40 219990002 34.57 34 40 40 6 25 40 1522515 1125455 2159183 1555765 73 - 18 6362991 -5 40 214104778 33.65 30 40 40 10 15 40 1479795 2068113 1558400 1249337 7346 - 19 6362991 -5 40 212934712 33.46 30 40 40 10 15 40 1432749 1231352 1769799 1920093 8998 - 20 6362991 -5 40 212787944 33.44 29 40 40 11 13 40 1311657 1411663 2126316 1513282 73 - 21 6362991 -5 40 211369187 33.22 28 40 40 12 10 40 1887985 1846300 1300326 1318380 10000 - 22 6362991 -5 40 213371720 33.53 30 40 40 10 15 40 542299 3446249 516615 1848190 9638 - 23 6362991 -5 40 221975899 34.89 36 40 40 4 30 40 347679 1233267 926621 3855355 69 - 24 6362991 -5 40 194378421 30.55 21 40 40 19 -5 40 433560 674358 3262764 1992242 67 - 25 6362991 -5 40 199773985 31.40 23 40 40 17 -2 40 944760 325595 1322800 3769641 195 - 26 6362991 -5 40 179404759 28.20 17 34 40 23 -5 40 3457922 156013 1494664 1254293 99 - 27 6362991 -5 40 163386668 25.68 13 28 40 27 -5 40 1392177 281250 3867895 821491 178 - 28 6362991 -5 40 156230534 24.55 12 25 40 28 -5 40 907189 981249 4174945 299437 171 - 29 6362991 -5 40 163236046 25.65 13 28 40 27 -5 40 1097171 3418678 1567013 280008 121 - 30 6362991 -5 40 151309826 23.78 12 23 40 28 -5 40 3514775 2036194 566277 245613 132 - 31 6362991 -5 40 141392520 22.22 10 21 40 30 -5 40 1569000 4571357 124732 97721 181 - 32 6362991 -5 40 143436943 22.54 10 21 40 30 -5 40 1453607 4519441 38176 351107 660 - 33 6362991 -5 40 114269843 17.96 6 14 30 24 -5 40 3311001 2161254 155505 734297 934 - 34 6362991 -5 40 140638447 22.10 10 20 40 30 -5 40 1501615 1637357 18113 3205237 669 - 35 6362991 -5 40 138910532 21.83 10 20 40 30 -5 40 1532519 3495057 23229 1311834 352 - 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 - - -</help> -</tool> - diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastq_quality_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,88 @@ +<tool id="cshl_fastq_quality_converter" name="Quality format converter"> + <description>(ASCII-Numeric)</description> + <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> + <inputs> + <param format="fastqsolexa" name="input" type="data" label="Library to convert" /> + + <param name="QUAL_FORMAT" type="select" label="Desired output format"> + <option value="-a">ASCII (letters) quality scores</option> + <option value="-n">Numeric quality scores</option> + </param> + + <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> + </inputs> + + <tests> + <test> +  + <param name="input" value="fastq_qual_conv1.fastq" /> + <param name="QUAL_FORMAT" value="Numeric quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv1.out" /> + </test> + <test> +  + <param name="input" value="fastq_qual_conv1.fastq" /> + <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv1a.out" /> + </test> + <test> +  + <param name="input" value="fastq_qual_conv2.fastq" /> + <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv2.out" /> + </test> + <test> +  + <param name="input" value="fastq_qual_conv2.fastq" /> + <param name="QUAL_FORMAT" value="Numeric quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv2n.out" /> + </test> + </tests> + + <outputs> + <data format="fastqsolexa" name="output" metadata_source="input" /> + </outputs> +<help> + +**What it does** + +Converts a solexa FASTQ file to/from numeric or ASCII quality format. + +.. class:: warningmark + +Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). + + +----- + +FASTQ with Numeric quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 + + +FASTQ with ASCII quality scores:: + + @CSHL__2_FC042AGWWWXX:8:1:120:202 + ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC + +CSHL__2_FC042AGWWWXX:8:1:120:202 + hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH + @CSHL__2_FC042AGWWWXX:8:1:103:1185 + ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC + +CSHL__2_FC042AGWWWXX:8:1:103:1185 + hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B + + +</help> +</tool> + diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_barcode_splitter.xml --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml Mon Sep 14 15:27:55 2009 -0400 +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml Mon Sep 14 17:03:17 2009 -0400 @@ -1,6 +1,6 @@ <tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter"> <description></description> - <command>fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" --mismatches $mismatches --partial $partial $EOL > $output </command> + <command interpreter="sh">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> <inputs> <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> @@ -61,7 +61,7 @@ **Output Example** -.. image:: ../static/fastx_icons/barcode_splitter_output_example.png +.. image:: ./static/fastx_icons/barcode_splitter_output_example.png </help> </tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,80 @@ +#!/bin/sh + +# FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon(a)cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +# +#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# +# 1. Output files are saved at the dataset's files_path directory. +# +# 2. 'fastx_barcode_splitter.pl' outputs a textual table. +# This script turns it into pretty HTML with working URL +# (so lazy users can just click on the URLs and get their files) + +BARCODE_FILE="$1" +FASTQ_FILE="$2" +LIBNAME="$3" +OUTPUT_PATH="$4" +shift 4 +# The rest of the parameters are passed to the split program + +if [ "$OUTPUT_PATH" == "" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 + exit 1 +fi + +#Sanitize library name, make sure we can create a file with this name +LIBNAME=${LIBNAME//\.gz/} +LIBNAME=${LIBNAME//\.txt/} +LIBNAME=${LIBNAME//[^[:alnum:]]/_} + +if [ ! -r "$FASTQ_FILE" ]; then + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 +fi +if [ ! -r "$BARCODE_FILE" ]; then + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 +fi +mkdir -p "$OUTPUT_PATH" +if [ ! -d "$OUTPUT_PATH" ]; then + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 +fi + +PUBLICURL="" +BASEPATH="$OUTPUT_PATH/" +#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" +PREFIX="$BASEPATH""${LIBNAME}__" +SUFFIX=".txt" + +RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +if [ $? != 0 ]; then + echo "error" +fi + +# +# Convert the textual tab-separated table into simple HTML table, +# with the local path replaces with a valid URL +echo "<html><body><table border=1>" +echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|<a href=\"\\1\">\\1</a>|" | sed ' +i<tr><td> +s|\t|</td><td>|g +a<\/td><\/tr> +' +echo "<p>" +echo "</table></body></html>" diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_clipper.xml --- a/tools/fastx_toolkit/fastx_clipper.xml Mon Sep 14 15:27:55 2009 -0400 +++ b/tools/fastx_toolkit/fastx_clipper.xml Mon Sep 14 17:03:17 2009 -0400 @@ -1,15 +1,11 @@ <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" > <description>adapter sequences</description> <command> - zcat -f $input | fastx_clipper -s $maxmismatches -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS + zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS </command> <inputs> <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" /> - - <param name="maxmismatches" size="4" type="integer" value="2"> - <label>Maximum number of mismatches allowed (when matching the adapter sequence)</label> - </param> <param name="minlength" size="4" type="integer" value="15"> <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> @@ -52,22 +48,23 @@ </param> </inputs> - +  <param name="input" value="fastx_clipper1.fastq" /> <param name="maxmismatches" value="2" /> <param name="minlength" value="15" /> - <param name="clip_source.clip_source_list" value="user" /> - <param name="clip_source.clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> + <param name="clip_source_list" value="user" /> + <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> <param name="keepdelta" value="0" /> <param name="KEEP_N" value="-n" /> <param name="DISCARD_OPTIONS" value="-c" /> <output name="output" file="fastx_clipper1a.out" /> </test> </tests> - + --> <outputs> <data format="input" name="output" metadata_source="input" /> </outputs> @@ -82,7 +79,7 @@ **Clipping Illustration:** -.. image:: ../static/fastx_icons/fastx_clipper_illustration.png +.. image:: ./static/fastx_icons/fastx_clipper_illustration.png @@ -93,7 +90,7 @@ **Clipping Example:** -.. image:: ../static/fastx_icons/fastx_clipper_example.png +.. image:: ./static/fastx_icons/fastx_clipper_example.png diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_collapser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastx_collapser.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,75 @@ +<tool id="cshl_fastx_collapser" name="Collapse"> + <description>sequences</description> + <command>zcat -f '$input' | fastx_collapser -v -o '$output' </command> + + <inputs> + <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" /> + </inputs> + + <tests> + <test> + <param name="input" value="fasta_collapser1.fasta" /> + <output name="output" file="fasta_collapser1.out" /> + </test> + </tests> + + <outputs> + <data format="fasta" name="output" metadata_source="input" /> + </outputs> + <help> + +**What it does** + +This tool collapses identical sequences in a FASTA file into a single sequence. + +-------- + +**Example** + +Example Input File (Sequence "ATAT" appears multiple times):: + + >CSHL_2_FC0042AGLLOO_1_1_605_414 + TGCG + >CSHL_2_FC0042AGLLOO_1_1_537_759 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_774_520 + TGGC + >CSHL_2_FC0042AGLLOO_1_1_742_502 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_781_514 + TGAG + >CSHL_2_FC0042AGLLOO_1_1_757_487 + TTCA + >CSHL_2_FC0042AGLLOO_1_1_903_769 + ATAT + >CSHL_2_FC0042AGLLOO_1_1_724_499 + ATAT + +Example Output file:: + + >1-1 + TGCG + >2-4 + ATAT + >3-1 + TGGC + >4-1 + TGAG + >5-1 + TTCA + +.. class:: infomark + +Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. + +The output seqeunce name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. + +The following output:: + + >2-4 + ATAT + +means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. + +</help> +</tool> diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_nucleotides_distribution.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,66 @@ +<tool id="cshl_fastx_nucleotides_distribution" name="Nucleotides Distribution"> + <description>chart</description> + <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command> + + <inputs> + <param format="txt" name="input" type="data" label="Statistics Text File (output of 'FASTX Statistics' tool)" /> + </inputs> + + <outputs> + <data format="png" name="output" metadata_source="input" /> + </outputs> +<help> + +**What it does** + +Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. + +.. class:: infomark + +**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. + +----- + +**Output Examples** + + + +The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** + +.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png + + + + + + + +In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** + +.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png + + + + + + + + +The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): + +.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png + + + + + + + + +But most of the time, the chart will look rather random: + +.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png + +</help> +</tool> + diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_quality_statistics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,102 @@ +<tool id="cshl_fastx_quality_statistics" name="Quality Statistics"> + <description></description> + <command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command> + + <inputs> + <param format="fasta,fastqsolexa" name="input" type="data" label="Library to analyse" /> + <param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" /> + </inputs> + + <tests> + <test> + <param name="input" value="fastq_stats1.fastq" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_stats1.out" /> + </test> + </tests> + + <outputs> + <data format="txt" name="output" metadata_source="input" /> + </outputs> + +<help> + +**What it does** + +Creates quality statistics report for the given Solexa/FASTQ library. + +.. class:: infomark + +**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. + +----- + +**The output file will contain the following fields:** + +* column = column number (1 to 36 for a 36-cycles read solexa file) +* count = number of bases found in this column. +* min = Lowest quality score value found in this column. +* max = Highest quality score value found in this column. +* sum = Sum of quality score values for this column. +* mean = Mean quality score value for this column. +* Q1 = 1st quartile quality score. +* med = Median quality score. +* Q3 = 3rd quartile quality score. +* IQR = Inter-Quartile range (Q3-Q1). +* lW = 'Left-Whisker' value (for boxplotting). +* rW = 'Right-Whisker' value (for boxplotting). +* A_Count = Count of 'A' nucleotides found in this column. +* C_Count = Count of 'C' nucleotides found in this column. +* G_Count = Count of 'G' nucleotides found in this column. +* T_Count = Count of 'T' nucleotides found in this column. +* N_Count = Count of 'N' nucleotides found in this column. + + + + + + +**Output Example**:: + + column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count + 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 + 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 + 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 + 4 6362991 -5 40 247654797 38.92 40 40 40 0 40 40 1683197 1410855 1722633 1546306 0 + 5 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 + 6 6362991 -5 40 248499903 39.05 40 40 40 0 40 40 1598956 1236081 1568608 1959346 0 + 7 6362991 -4 40 247719760 38.93 40 40 40 0 40 40 1692667 1822140 1496741 1351443 0 + 8 6362991 -5 40 245745205 38.62 40 40 40 0 40 40 2230936 1343260 1529928 1258867 0 + 9 6362991 -5 40 245766735 38.62 40 40 40 0 40 40 1702064 1306257 1336511 2018159 0 + 10 6362991 -5 40 245089706 38.52 40 40 40 0 40 40 1519917 1446370 1450995 1945709 0 + 11 6362991 -5 40 242641359 38.13 40 40 40 0 40 40 1717434 1282975 1387804 1974778 0 + 12 6362991 -5 40 242026113 38.04 40 40 40 0 40 40 1662872 1202041 1519721 1978357 0 + 13 6362991 -5 40 238704245 37.51 40 40 40 0 40 40 1549965 1271411 1973291 1566681 1643 + 14 6362991 -5 40 235622401 37.03 40 40 40 0 40 40 2101301 1141451 1603990 1515774 475 + 15 6362991 -5 40 230766669 36.27 40 40 40 0 40 40 2344003 1058571 1440466 1519865 86 + 16 6362991 -5 40 224466237 35.28 38 40 40 2 35 40 2203515 1026017 1474060 1651582 7817 + 17 6362991 -5 40 219990002 34.57 34 40 40 6 25 40 1522515 1125455 2159183 1555765 73 + 18 6362991 -5 40 214104778 33.65 30 40 40 10 15 40 1479795 2068113 1558400 1249337 7346 + 19 6362991 -5 40 212934712 33.46 30 40 40 10 15 40 1432749 1231352 1769799 1920093 8998 + 20 6362991 -5 40 212787944 33.44 29 40 40 11 13 40 1311657 1411663 2126316 1513282 73 + 21 6362991 -5 40 211369187 33.22 28 40 40 12 10 40 1887985 1846300 1300326 1318380 10000 + 22 6362991 -5 40 213371720 33.53 30 40 40 10 15 40 542299 3446249 516615 1848190 9638 + 23 6362991 -5 40 221975899 34.89 36 40 40 4 30 40 347679 1233267 926621 3855355 69 + 24 6362991 -5 40 194378421 30.55 21 40 40 19 -5 40 433560 674358 3262764 1992242 67 + 25 6362991 -5 40 199773985 31.40 23 40 40 17 -2 40 944760 325595 1322800 3769641 195 + 26 6362991 -5 40 179404759 28.20 17 34 40 23 -5 40 3457922 156013 1494664 1254293 99 + 27 6362991 -5 40 163386668 25.68 13 28 40 27 -5 40 1392177 281250 3867895 821491 178 + 28 6362991 -5 40 156230534 24.55 12 25 40 28 -5 40 907189 981249 4174945 299437 171 + 29 6362991 -5 40 163236046 25.65 13 28 40 27 -5 40 1097171 3418678 1567013 280008 121 + 30 6362991 -5 40 151309826 23.78 12 23 40 28 -5 40 3514775 2036194 566277 245613 132 + 31 6362991 -5 40 141392520 22.22 10 21 40 30 -5 40 1569000 4571357 124732 97721 181 + 32 6362991 -5 40 143436943 22.54 10 21 40 30 -5 40 1453607 4519441 38176 351107 660 + 33 6362991 -5 40 114269843 17.96 6 14 30 24 -5 40 3311001 2161254 155505 734297 934 + 34 6362991 -5 40 140638447 22.10 10 20 40 30 -5 40 1501615 1637357 18113 3205237 669 + 35 6362991 -5 40 138910532 21.83 10 20 40 30 -5 40 1532519 3495057 23229 1311834 352 + 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 + + +</help> +</tool> + diff -r 0f97b3048bc3 -r 40c5e1853a66 tools/fastx_toolkit/fastx_renamer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastx_toolkit/fastx_renamer.xml Mon Sep 14 17:03:17 2009 -0400 @@ -0,0 +1,56 @@ +<tool id="cshl_fastx_renamer" name="Rename" version="0.0.11" > + <description>sequence identifiers</description> + <command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command> + + <inputs> + <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" /> + + <param name="TYPE" type="select" label="Rename sequence identifiers to"> + <option value="SEQ">Nucleotides sequence</option> + <option value="COUNT">Numeric Counter</option> + </param> + </inputs> + + <outputs> + <data format="input" name="output" metadata_source="input" /> + </outputs> + +<help> + +**What it does** + +This tool renames the sequence identifiers in a FASTQ/A file. + +.. class:: infomark + +Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming,clipping,barcode-removal, etc). + +-------- + +**Example** + +The following Solexa-FASTQ file:: + + @CSHL_4_FC042GAMMII_2_1_517_596 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +CSHL_4_FC042GAMMII_2_1_517_596 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **nucleotides sequence**:: + + @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + +Renamed to **numeric counter**:: + + @1 + GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT + +1 + 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 + + +</help> +</tool> +

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[hg] galaxy 2690: Modifications for fastq splitted help
by Greg Von Kuster 14 Sep '09

14 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0f97b3048bc3 changeset: 2690:0f97b3048bc3 user: anton(a)nekrut-mbp.bx.psu.edu date: Mon Sep 14 15:27:55 2009 -0400 description: Modifications for fastq splitted help 2 file(s) affected in this change: tool_conf.xml.sample tools/metag_tools/split_paired_reads.xml diffs (23 lines): diff -r e58e140b89f7 -r 0f97b3048bc3 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Sep 14 14:54:11 2009 -0400 +++ b/tool_conf.xml.sample Mon Sep 14 15:27:55 2009 -0400 @@ -338,6 +338,7 @@ <tool file="visualization/genetrack.xml" /> </section> <section name="SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> <tool file="samtools/sam_to_bam.xml" /> <tool file="samtools/sam_merge.xml" /> <tool file="samtools/sam_pileup.xml" /> diff -r e58e140b89f7 -r 0f97b3048bc3 tools/metag_tools/split_paired_reads.xml --- a/tools/metag_tools/split_paired_reads.xml Mon Sep 14 14:54:11 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.xml Mon Sep 14 15:27:55 2009 -0400 @@ -20,7 +20,7 @@ **What it does** -This tool splits a single paired-end file in half and returns two files with each ends. +Splits a single fastq datasret representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length. -----

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