Mercurial > repos > rmarenco > hubarchivecreator
view BedSimpleRepeats.py @ 14:cbd8982c9f51 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 38f01a73fea83321618501978a3a505b5e8ab527
author | rmarenco |
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date | Mon, 15 Aug 2016 19:19:32 -0400 |
parents | 25809f699cb3 |
children | 3233451a3bd6 |
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#!/usr/bin/python import os import tempfile from Datatype import Datatype from Track import Track from TrackDb import TrackDb from util import subtools class BedSimpleRepeats( Datatype ): def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats): super(BedSimpleRepeats, self).__init__() self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path self.name_bed_simple_repeats = data_bed_simple_repeats["name"] self.priority = data_bed_simple_repeats["order_index"] sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") # Sort processing subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) # bedToBigBed processing # TODO: Change the name of the bb, to tool + genome + .bb trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) ) myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as') with open(myBigBedFilePath, 'w') as bigBedFile: subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name, typeOption='bed4+12', autoSql=auto_sql_option) # Create the Track Object self.createTrack(file_path=trackName, track_name=trackName, long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', priority=self.priority, track_file=myBigBedFilePath) # dataURL = "tracks/%s" % trackName # # trackDb = TrackDb( # trackName=trackName, # longLabel=self.name_bed_simple_repeats, # shortLabel=self.getShortName( self.name_bed_simple_repeats ), # trackDataURL=dataURL, # trackType='bigBed 4 +', # visibility='dense', # priority=self.priority, # ) # # self.track = Track( # trackFile=myBigBedFilePath, # trackDb=trackDb, # ) print("- Bed simple repeats %s created" % self.name_bed_simple_repeats) #print("- %s created in %s" % (trackName, myBigBedFilePath))