Mercurial > repos > rmarenco > hubarchivecreator
comparison BedSimpleRepeats.py @ 13:25809f699cb3 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author | rmarenco |
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date | Thu, 11 Aug 2016 19:02:29 -0400 |
parents | d05236b15f81 |
children | 3233451a3bd6 |
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12:747475757cb0 | 13:25809f699cb3 |
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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, |