Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.py @ 11:d05236b15f81 draft

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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
comparison
equal deleted inserted replaced
10:acc233161f50 11:d05236b15f81
45 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 45 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
46 with open(myBigBedFilePath, 'w') as bigBedFile: 46 with open(myBigBedFilePath, 'w') as bigBedFile:
47 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) 47 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
48 48
49 # Create the Track Object 49 # Create the Track Object
50 dataURL = "tracks/%s" % trackName 50 self.createTrack(file_path=trackName,
51 track_name=trackName,
52 long_label=self.name_gff3, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
53 track_file=myBigBedFilePath)
51 54
52 trackDb = TrackDb( 55 # dataURL = "tracks/%s" % trackName
53 trackName=trackName, 56 #
54 longLabel=self.name_gff3, 57 # trackDb = TrackDb(
55 shortLabel=self.getShortName( self.name_gff3 ), 58 # trackName=trackName,
56 trackDataURL=dataURL, 59 # longLabel=self.name_gff3,
57 trackType='bigBed 12 +', 60 # shortLabel=self.getShortName( self.name_gff3 ),
58 visibility='dense', 61 # trackDataURL=dataURL,
59 priority=self.priority, 62 # trackType='bigBed 12 +',
60 ) 63 # visibility='dense',
64 # priority=self.priority,
65 # )
66 #
67 # self.track = Track(
68 # trackFile=myBigBedFilePath,
69 # trackDb=trackDb,
70 # )
61 71
62 self.track = Track( 72 print("- Gff3 %s created" % self.name_gff3)
63 trackFile=myBigBedFilePath, 73 #print("- %s created in %s" % (trackName, myBigBedFilePath))
64 trackDb=trackDb,
65 )
66
67 print("- %s created in %s" % (trackName, myBigBedFilePath))