Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSimpleRepeats.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children 3233451a3bd6
comparison
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12:747475757cb0 13:25809f699cb3
25 25
26 # bedToBigBed processing 26 # bedToBigBed processing
27 # TODO: Change the name of the bb, to tool + genome + .bb 27 # TODO: Change the name of the bb, to tool + genome + .bb
28 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) ) 28 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
29 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 29 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
30 auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as')) 30
31 auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
32
31 with open(myBigBedFilePath, 'w') as bigBedFile: 33 with open(myBigBedFilePath, 'w') as bigBedFile:
32 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name, 34 subtools.bedToBigBed(sortedBedFile.name,
33 typeOption='-type=bed4+12', 35 self.chromSizesFile.name,
36 bigBedFile.name,
37 typeOption='bed4+12',
34 autoSql=auto_sql_option) 38 autoSql=auto_sql_option)
35 39
36 # Create the Track Object 40 # Create the Track Object
37 self.createTrack(file_path=trackName, 41 self.createTrack(file_path=trackName,
38 track_name=trackName, 42 track_name=trackName,