Mercurial > repos > rmarenco > hubarchivecreator
diff Gtf.py @ 11:d05236b15f81 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
| author | rmarenco |
|---|---|
| date | Wed, 27 Jul 2016 10:10:49 -0400 |
| parents | acc233161f50 |
| children | 25809f699cb3 |
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--- a/Gtf.py Thu Jul 21 05:58:51 2016 -0400 +++ b/Gtf.py Wed Jul 27 10:10:49 2016 -0400 @@ -21,7 +21,7 @@ self.name_gtf = data_gtf["name"] self.priority = data_gtf["order_index"] - print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) + #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) # TODO: See if we need these temporary files as part of the generated files genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") @@ -46,20 +46,26 @@ subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) # Create the Track Object - dataURL = "tracks/%s" % trackName + self.createTrack(file_path=trackName, + track_name=trackName, + long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority, + track_file=myBigBedFilePath) + # + # dataURL = "tracks/%s" % trackName + # + # trackDb = TrackDb( + # trackName=trackName, + # longLabel=self.name_gtf, + # shortLabel=self.getShortName( self.name_gtf ), + # trackDataURL=dataURL, + # trackType='bigBed 12 +', + # visibility='dense', + # priority=self.priority, + # ) + # self.track = Track( + # trackFile=myBigBedFilePath, + # trackDb=trackDb, + # ) - trackDb = TrackDb( - trackName=trackName, - longLabel=self.name_gtf, - shortLabel=self.getShortName( self.name_gtf ), - trackDataURL=dataURL, - trackType='bigBed 12 +', - visibility='dense', - priority=self.priority, - ) - self.track = Track( - trackFile=myBigBedFilePath, - trackDb=trackDb, - ) - - print("- %s created in %s" % (trackName, myBigBedFilePath)) + print("- Gtf %s created" % self.name_gtf) + #print("- %s created in %s" % (trackName, myBigBedFilePath))