Mercurial > repos > rmarenco > hubarchivecreator
comparison BedSimpleRepeats.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
| author | rmarenco |
|---|---|
| date | Wed, 13 Jul 2016 13:36:37 -0400 |
| parents | |
| children | acc233161f50 |
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| 0:0f3bc17e5ede | 1:fb5e60d4d18a |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import tempfile | |
| 5 | |
| 6 from Datatype import Datatype | |
| 7 from Track import Track | |
| 8 from TrackDb import TrackDb | |
| 9 from util import subtools | |
| 10 | |
| 11 | |
| 12 class BedSimpleRepeats( Datatype ): | |
| 13 def __init__( self, input_bed_simple_repeats_false_path, data_bed_simple_repeats, | |
| 14 input_fasta_file, extra_files_path, tool_directory ): | |
| 15 | |
| 16 super(BedSimpleRepeats, self).__init__( | |
| 17 input_fasta_file, extra_files_path, tool_directory | |
| 18 ) | |
| 19 | |
| 20 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path | |
| 21 self.name_bed_simple_repeats = data_bed_simple_repeats["name"] | |
| 22 self.priority = data_bed_simple_repeats["order_index"] | |
| 23 | |
| 24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | |
| 25 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) | |
| 26 chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") | |
| 27 | |
| 28 # Sort processing | |
| 29 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) | |
| 30 | |
| 31 # TODO: Regroup in an mother class which handles the Chrom.sizes creation with Gff3 and Gtf | |
| 32 # Generate the chrom.sizes | |
| 33 | |
| 34 subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name) | |
| 35 | |
| 36 # Then we get the output to inject into the sort | |
| 37 # TODO: Check if no errors | |
| 38 subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name) | |
| 39 | |
| 40 # bedToBigBed processing | |
| 41 # TODO: Change the name of the bb, to tool + genome + .bb | |
| 42 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) ) | |
| 43 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 44 auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as')) | |
| 45 with open(myBigBedFilePath, 'w') as bigBedFile: | |
| 46 subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name, | |
| 47 typeOption='-type=bed4+12', | |
| 48 autoSql=auto_sql_option) | |
| 49 | |
| 50 # Create the Track Object | |
| 51 dataURL = "tracks/%s" % trackName | |
| 52 | |
| 53 trackDb = TrackDb( | |
| 54 trackName=trackName, | |
| 55 longLabel=self.name_bed_simple_repeats, | |
| 56 shortLabel=self.getShortName( self.name_bed_simple_repeats ), | |
| 57 trackDataURL=dataURL, | |
| 58 trackType='bigBed 4 +', | |
| 59 visibility='dense', | |
| 60 priority=self.priority, | |
| 61 ) | |
| 62 | |
| 63 self.track = Track( | |
| 64 trackFile=myBigBedFilePath, | |
| 65 trackDb=trackDb, | |
| 66 ) | |
| 67 | |
| 68 print("- %s created in %s" % (trackName, myBigBedFilePath)) |