Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSimpleRepeats.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
32 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name, 32 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
33 typeOption='-type=bed4+12', 33 typeOption='-type=bed4+12',
34 autoSql=auto_sql_option) 34 autoSql=auto_sql_option)
35 35
36 # Create the Track Object 36 # Create the Track Object
37 dataURL = "tracks/%s" % trackName 37 self.createTrack(file_path=trackName,
38 track_name=trackName,
39 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
40 priority=self.priority,
41 track_file=myBigBedFilePath)
38 42
39 trackDb = TrackDb( 43 # dataURL = "tracks/%s" % trackName
40 trackName=trackName, 44 #
41 longLabel=self.name_bed_simple_repeats, 45 # trackDb = TrackDb(
42 shortLabel=self.getShortName( self.name_bed_simple_repeats ), 46 # trackName=trackName,
43 trackDataURL=dataURL, 47 # longLabel=self.name_bed_simple_repeats,
44 trackType='bigBed 4 +', 48 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
45 visibility='dense', 49 # trackDataURL=dataURL,
46 priority=self.priority, 50 # trackType='bigBed 4 +',
47 ) 51 # visibility='dense',
52 # priority=self.priority,
53 # )
54 #
55 # self.track = Track(
56 # trackFile=myBigBedFilePath,
57 # trackDb=trackDb,
58 # )
48 59
49 self.track = Track( 60 print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
50 trackFile=myBigBedFilePath, 61 #print("- %s created in %s" % (trackName, myBigBedFilePath))
51 trackDb=trackDb,
52 )
53
54 print("- %s created in %s" % (trackName, myBigBedFilePath))