Mercurial > repos > rmarenco > hubarchivecreator
view Bed.py @ 23:2677f1899aa8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author | yating-l |
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date | Tue, 09 May 2017 15:42:43 -0400 |
parents | c02720d1afee |
children | df42241d3731 |
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#!/usr/bin/python import os import tempfile # Internal dependencies from Datatype import Datatype from Track import Track from TrackDb import TrackDb from util import subtools class Bed( Datatype ): def __init__( self, inputBedGeneric, data_bed_generic): super(Bed, self).__init__() self.track = None self.inputBedGeneric = inputBedGeneric self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") self.data_bed_generic = data_bed_generic self.name_bed_generic = self.data_bed_generic["name"] self.priority = self.data_bed_generic["order_index"] self.track_color = self.data_bed_generic["track_color"] # TODO: Think about how to avoid repetition of the group_name everywhere self.group_name = self.data_bed_generic["group_name"] if self.data_bed_generic["long_label"]: self.long_label = self.data_bed_generic["long_label"] else: self.long_label = self.name_bed_generic # Sort processing subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) # bedToBigBed processing # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb trackName = "".join( ( self.name_bed_generic, ".bb") ) myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) with open(myBigBedFilePath, 'w') as self.bigBedFile: subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name) # Create the Track Object self.createTrack(file_path=trackName, track_name=trackName, long_label=self.long_label, track_type='bigBed', visibility='dense', priority=self.priority, track_file=myBigBedFilePath, track_color=self.track_color, group_name=self.group_name) # dataURL = "tracks/%s" % trackName # # trackDb = TrackDb( # trackName=trackName, # longLabel=self.name_bed_generic, # shortLabel=self.getShortName(self.name_bed_generic), # trackDataURL=dataURL, # trackType='bigBed', # visibility='dense', # thickDrawItem='on', # priority=self.priority, # ) # # # Return the BigBed track # self.track = Track( # trackFile=myBigBedFilePath, # trackDb=trackDb, # ) print("- Bed %s created" % self.name_bed_generic) #print("- %s created in %s" % (trackName, myBigBedFilePath))