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annotate Gtf.py @ 12:747475757cb0 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 85389def8ed35b3dc08701963dcae4afd1b5b50a
author rmarenco
date Wed, 27 Jul 2016 10:43:58 -0400
parents d05236b15f81
children 25809f699cb3
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1 #!/usr/bin/python
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3 import os
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4 import tempfile
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6 # Internal dependencies
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7 from Datatype import Datatype
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8 from Track import Track
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9 from TrackDb import TrackDb
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10 from util import subtools
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13 class Gtf( Datatype ):
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14 def __init__( self, input_gtf_false_path, data_gtf):
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16 super(Gtf, self).__init__()
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18 self.track = None
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20 self.input_gtf_false_path = input_gtf_false_path
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21 self.name_gtf = data_gtf["name"]
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22 self.priority = data_gtf["order_index"]
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24 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
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26 # TODO: See if we need these temporary files as part of the generated files
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27 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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28 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
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29 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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31 # GtfToGenePred
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32 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
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34 # TODO: From there, refactor because common use with Gff3.py
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35 # genePredToBed processing
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36 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
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38 # Sort processing
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39 subtools.sort(unsortedBedFile.name, sortedBedFile.name)
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41 # bedToBigBed processing
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42 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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43 trackName = "".join( ( self.name_gtf, ".bb") )
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44 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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45 with open(myBigBedFilePath, 'w') as bigBedFile:
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46 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
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48 # Create the Track Object
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49 self.createTrack(file_path=trackName,
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50 track_name=trackName,
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51 long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
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52 track_file=myBigBedFilePath)
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53 #
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54 # dataURL = "tracks/%s" % trackName
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55 #
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56 # trackDb = TrackDb(
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57 # trackName=trackName,
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58 # longLabel=self.name_gtf,
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59 # shortLabel=self.getShortName( self.name_gtf ),
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60 # trackDataURL=dataURL,
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61 # trackType='bigBed 12 +',
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62 # visibility='dense',
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63 # priority=self.priority,
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64 # )
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65 # self.track = Track(
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66 # trackFile=myBigBedFilePath,
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67 # trackDb=trackDb,
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68 # )
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69
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70 print("- Gtf %s created" % self.name_gtf)
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71 #print("- %s created in %s" % (trackName, myBigBedFilePath))