Mercurial > repos > rmarenco > hubarchivecreator

comparison Bed.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
34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
35 with open(myBigBedFilePath, 'w') as self.bigBedFile: 35 with open(myBigBedFilePath, 'w') as self.bigBedFile:
36 subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name) 36 subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
37 37
38 # Create the Track Object 38 # Create the Track Object
39 dataURL = "tracks/%s" % trackName 39 self.createTrack(file_path=trackName,
40 track_name=trackName,
41 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
42 priority=self.priority,
43 track_file=myBigBedFilePath)
40 44
41 trackDb = TrackDb( 45 # dataURL = "tracks/%s" % trackName
42 trackName=trackName, 46 #
43 longLabel=self.name_bed_generic, 47 # trackDb = TrackDb(
44 shortLabel=self.getShortName(self.name_bed_generic), 48 # trackName=trackName,
45 trackDataURL=dataURL, 49 # longLabel=self.name_bed_generic,
46 trackType='bigBed', 50 # shortLabel=self.getShortName(self.name_bed_generic),
47 visibility='dense', 51 # trackDataURL=dataURL,
48 thickDrawItem='on', 52 # trackType='bigBed',
49 priority=self.priority, 53 # visibility='dense',
50 ) 54 # thickDrawItem='on',
55 # priority=self.priority,
56 # )
57 #
58 # # Return the BigBed track
59 # self.track = Track(
60 # trackFile=myBigBedFilePath,
61 # trackDb=trackDb,
62 # )
51 63
52 # Return the BigBed track 64 print("- Bed %s created" % self.name_bed_generic)
53 self.track = Track( 65 #print("- %s created in %s" % (trackName, myBigBedFilePath))
54 trackFile=myBigBedFilePath,
55 trackDb=trackDb,
56 )
57
58 print("- %s created in %s" % (trackName, myBigBedFilePath))