Mercurial > repos > rmarenco > hubarchivecreator

comparison Gtf.py @ 11:d05236b15f81 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author rmarenco
date Wed, 27 Jul 2016 10:10:49 -0400
parents acc233161f50
children 25809f699cb3
comparison
equal deleted inserted replaced
10:acc233161f50 11:d05236b15f81
19 19
20 self.input_gtf_false_path = input_gtf_false_path 20 self.input_gtf_false_path = input_gtf_false_path
21 self.name_gtf = data_gtf["name"] 21 self.name_gtf = data_gtf["name"]
22 self.priority = data_gtf["order_index"] 22 self.priority = data_gtf["order_index"]
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 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
29 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 29 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
44 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 44 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
45 with open(myBigBedFilePath, 'w') as bigBedFile: 45 with open(myBigBedFilePath, 'w') as bigBedFile:
46 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) 46 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
47 47
48 # Create the Track Object 48 # Create the Track Object
49 dataURL = "tracks/%s" % trackName 49 self.createTrack(file_path=trackName,
50 track_name=trackName,
51 long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
52 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 # )
50 69
51 trackDb = TrackDb( 70 print("- Gtf %s created" % self.name_gtf)
52 trackName=trackName, 71 #print("- %s created in %s" % (trackName, myBigBedFilePath))
53 longLabel=self.name_gtf,
54 shortLabel=self.getShortName( self.name_gtf ),
55 trackDataURL=dataURL,
56 trackType='bigBed 12 +',
57 visibility='dense',
58 priority=self.priority,
59 )
60 self.track = Track(
61 trackFile=myBigBedFilePath,
62 trackDb=trackDb,
63 )
64
65 print("- %s created in %s" % (trackName, myBigBedFilePath))