details: http://www.bx.psu.edu/hg/galaxy/rev/e7244f7d613b changeset: 3187:e7244f7d613b user: Kanwei Li kanwei@gmail.com date: Fri Dec 18 14:18:56 2009 -0500 description: Provide UCSC integration for GFF files. Closes #261

diffstat:

lib/galaxy/datatypes/interval.py | 65 ++++++++++++++++++++++---------- 1 files changed, 45 insertions(+), 20 deletions(-)

diffs (119 lines):

diff -r 1528580cc311 -r e7244f7d613b lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Dec 18 10:27:00 2009 -0500 +++ b/lib/galaxy/datatypes/interval.py Fri Dec 18 14:18:56 2009 -0500 @@ -485,7 +485,23 @@ return True except: return False

-class Gff( Tabular ): +class _RemoteCallMixin: + def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ): + """Retrieve the URL to call out to an external site and retrieve data. + This routes our external URL through a local galaxy instance which makes + the data available, followed by redirecting to the remote site with a + link back to the available information. + """ + internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='%s_%s' % ( type, site_name ) ) + base_url = app.config.get( "display_at_callback", base_url ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % \ + ( base_url, url_for( controller='root' ), dataset.id, type ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + return link + +class Gff( Tabular, _RemoteCallMixin ): """Tab delimited data in Gff format""" file_ext = "gff" column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] @@ -494,10 +510,11 @@ MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','str','str','int','int','int','str','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False )

- def __init__(self, **kwd): + def __init__( self, **kwd ): """Initialize datatype, by adding GBrowse display app""" Tabular.__init__(self, **kwd) - self.add_display_app ( 'c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' ) + self.add_display_app( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) + self.add_display_app( 'c_elegans', 'display in Wormbase', 'as_gbrowse_display_file', 'gbrowse_links' ) def set_meta( self, dataset, overwrite = True, **kwd ): i = 0 for i, line in enumerate( file ( dataset.file_name ) ): @@ -547,7 +564,13 @@ start = elems[2] # 6000000 stop = elems[3] # 6030000 break - if not line.startswith( '#' ): + # Allow UCSC style browser and track info in the GFF file + if line.startswith("browser position"): + pos_info = line.split()[-1] + seqid, startend = pos_info.split(":") + start, end = startend.split("-") + break + if not line.startswith(('#', 'track', 'browser')) : elems = line.split( '\t' ) if not seqid: # We can only set the viewport for a single chromosome @@ -566,6 +589,20 @@ return ( seqid, str( start ), str( stop ) ) else: return ( '', '', '' ) + def ucsc_links( self, dataset, type, app, base_url ): + ret_val = [] + if dataset.has_data: + seqid, start, stop = self.get_estimated_display_viewport( dataset ) + if seqid and start and stop: + for site_name, site_url in util.get_ucsc_by_build( dataset.dbkey ): + if site_name in app.config.ucsc_display_sites: + redirect_url = urllib.quote_plus( + "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % + ( site_url, dataset.dbkey, seqid, start, stop ) ) + link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) + ret_val.append( ( site_name, link ) ) + return ret_val + def gbrowse_links( self, dataset, type, app, base_url ): ret_val = [] if dataset.has_data: @@ -576,7 +613,9 @@ if seqid and start and stop: for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: - link = "%s?start=%s&stop=%s&ref=%s&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey ) + redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % + ( site_url, dataset.dbkey, seqid, start, stop ) ) + link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) return ret_val def sniff( self, filename ): @@ -728,7 +767,7 @@ except: return False

-class Wiggle( Tabular ): +class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format""" file_ext = "wig"

@@ -752,20 +791,6 @@ if i > num_check_lines: break return value - def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ): - """Retrieve the URL to call out to an external site and retrieve data. - This routes our external URL through a local galaxy instance which makes - the data available, followed by redirecting to the remote site with a - link back to the available information. - """ - internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='%s_%s' % ( type, site_name ) ) - base_url = app.config.get( "display_at_callback", base_url ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % \ - ( base_url, url_for( controller='root' ), dataset.id, type ) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - return link def _get_viewer_range( self, dataset ): """Retrieve the chromosome, start, end for an external viewer.""" if dataset.has_data: