Mercurial > repos > rmarenco > hubarchivecreator

comparison Gtf.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children 3233451a3bd6
comparison
equal deleted inserted replaced
12:747475757cb0 13:25809f699cb3
23 23
24 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) 24 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
25 25
26 # TODO: See if we need these temporary files as part of the generated files 26 # TODO: See if we need these temporary files as part of the generated files
27 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 27 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
28 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed") 28 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
29 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 29 sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred")
30 30
31 # GtfToGenePred 31 # GtfToGenePred
32 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name) 32 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
33 33
34 # TODO: From there, refactor because common use with Gff3.py 34 # TODO: From there, refactor because common use with Gff3.py
35 # genePredToBed processing 35 # genePredToBigGenePred processing
36 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name) 36 subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name)
37 37
38 # Sort processing 38 # Sort processing
39 subtools.sort(unsortedBedFile.name, sortedBedFile.name) 39 subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name)
40 40
41 # bedToBigBed processing 41 # bedToBigBed processing
42 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
43 trackName = "".join( ( self.name_gtf, ".bb") ) 42 trackName = "".join( ( self.name_gtf, ".bb") )
43
44 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
45
44 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 46 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
47
45 with open(myBigBedFilePath, 'w') as bigBedFile: 48 with open(myBigBedFilePath, 'w') as bigBedFile:
46 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) 49 subtools.bedToBigBed(sorted_bigGenePred_file.name,
50 self.chromSizesFile.name,
51 bigBedFile.name,
52 autoSql=auto_sql_option,
53 typeOption='bed12+8',
54 tab=True)
55
47 56
48 # Create the Track Object 57 # Create the Track Object
49 self.createTrack(file_path=trackName, 58 self.createTrack(file_path=trackName,
50 track_name=trackName, 59 track_name=trackName,
51 long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority, 60 long_label=self.name_gtf, track_type='bigGenePred',
61 visibility='dense', priority=self.priority,
52 track_file=myBigBedFilePath) 62 track_file=myBigBedFilePath)
53 #
54 # dataURL = "tracks/%s" % trackName
55 #
56 # trackDb = TrackDb(
57 # trackName=trackName,
58 # longLabel=self.name_gtf,
59 # shortLabel=self.getShortName( self.name_gtf ),
60 # trackDataURL=dataURL,
61 # trackType='bigBed 12 +',
62 # visibility='dense',
63 # priority=self.priority,
64 # )
65 # self.track = Track(
66 # trackFile=myBigBedFilePath,
67 # trackDb=trackDb,
68 # )
69 63
70 print("- Gtf %s created" % self.name_gtf) 64 print("- Gtf %s created" % self.name_gtf)
71 #print("- %s created in %s" % (trackName, myBigBedFilePath))