mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fixes for displaying appropriate datasets in GBrowse wormbase, modENCODE worm, and modENCODE fly.
This commit is contained in:
Greg Von Kuster
@@ -84,7 +84,7 @@ class Configuration( object ):
|
||||
self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
|
||||
self.bx_display_sites = kwargs.get( 'bx_display_sites', "main" ).lower().split(",")
|
||||
self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
|
||||
self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",")
|
||||
self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",")
|
||||
self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",")
|
||||
self.brand = kwargs.get( 'brand', None )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' )
|
||||
|
||||
@@ -582,7 +582,7 @@ class Gff( Tabular, _RemoteCallMixin ):
|
||||
"""Initialize datatype, by adding GBrowse display app"""
|
||||
Tabular.__init__(self, **kwd)
|
||||
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' )
|
||||
self.add_display_app( 'gbrowse', 'display in Gbrowse', '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 ) ):
|
||||
@@ -628,10 +628,24 @@ class Gff( Tabular, _RemoteCallMixin ):
|
||||
continue
|
||||
if line.startswith( '##sequence-region' ): # ##sequence-region IV 6000000 6030000
|
||||
elems = line.split()
|
||||
seqid = elems[1] # IV
|
||||
start = elems[2] # 6000000
|
||||
stop = elems[3] # 6030000
|
||||
break
|
||||
if len( elems ) > 3:
|
||||
# line looks like:
|
||||
# ##sequence-region ctg123 1 1497228
|
||||
seqid = elems[1] # IV
|
||||
start = elems[2] # 6000000
|
||||
stop = elems[3] # 6030000
|
||||
break
|
||||
elif len( elems ) == 2 and elems[1].find( '..' ) > 0:
|
||||
# line looks like this:
|
||||
# ##sequence-region X:120000..140000
|
||||
elems = elems[1].split( ':' )
|
||||
seqid = elems[0]
|
||||
start = elems[1].split( '..' )[0]
|
||||
stop = elems[1].split( '..' )[1]
|
||||
break
|
||||
else:
|
||||
log.exception( "line (%s) uses an unsupported ##sequence-region definition." % str( line ) )
|
||||
break
|
||||
# Allow UCSC style browser and track info in the GFF file
|
||||
if line.startswith("browser position"):
|
||||
pos_info = line.split()[-1]
|
||||
@@ -652,7 +666,8 @@ class Gff( Tabular, _RemoteCallMixin ):
|
||||
break
|
||||
if i > 10:
|
||||
break
|
||||
except:
|
||||
except Exception, e:
|
||||
log.exception( str( e ) )
|
||||
seqid, start, stop = ( '', '', '' )
|
||||
return ( seqid, str( start ), str( stop ) )
|
||||
else:
|
||||
@@ -681,8 +696,9 @@ class Gff( Tabular, _RemoteCallMixin ):
|
||||
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:
|
||||
redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" %
|
||||
( site_url, dataset.dbkey, seqid, start, stop ) )
|
||||
# Old method, the one uncommented below now seems to be the way GBrowse wants the request
|
||||
# redirect_url = urllib.quote_plus( "%s%s/?ref=%s&start=%s&stop=%s&eurl=%%s" % ( site_url, dataset.dbkey, seqid, start, stop ) )
|
||||
redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s" % ( site_url, 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
|
||||
|
||||
@@ -1,4 +1,11 @@
|
||||
# wormbase sites / supported genomes
|
||||
main http://www.wormbase.org/db/seq/gbgff/c_elegans/ c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi
|
||||
test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ c_elegans,c_briggsae,c_remanei,c_brenneri,c_japonica,p_pristionchus,b_malayi
|
||||
wormbase http://www.wormbase.org/db/gb2/gbrowse/c_elegans ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1
|
||||
#test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1
|
||||
|
||||
# UCSC mirror that includes arabidopsis
|
||||
tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis
|
||||
|
||||
# modENCODE worm and fly
|
||||
modencode_worm http://modencode.oicr.on.ca/fgb2/gbrowse/worm ce6
|
||||
modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2
|
||||
|
||||
|
||||
@@ -10,10 +10,12 @@
|
||||
<tool file="data_source/biomart.xml" />
|
||||
<tool file="data_source/biomart_test.xml" />
|
||||
<tool file="data_source/gramene_mart.xml" />
|
||||
<tool file="data_source/fly_modencode.xml" />
|
||||
<tool file="data_source/flymine.xml" />
|
||||
<tool file="data_source/flymine_test.xml" />
|
||||
<tool file="data_source/modmine.xml" />
|
||||
<tool file="data_source/ratmine.xml" />
|
||||
<tool file="data_source/worm_modencode.xml" />
|
||||
<tool file="data_source/wormbase.xml" />
|
||||
<tool file="data_source/wormbase_test.xml" />
|
||||
<tool file="data_source/eupathdb.xml" />
|
||||
|
||||
@@ -108,7 +108,7 @@ use_new_layout = true
|
||||
# Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing
|
||||
bx_display_sites = main
|
||||
ucsc_display_sites = main,test,archaea,ucla
|
||||
gbrowse_display_sites = main,test,tair
|
||||
gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly
|
||||
# Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt
|
||||
#genetrack_display_sites =
|
||||
|
||||
|
||||
Reference in New Issue
Block a user