Mercurial > repos > rmarenco > hubarchivecreator

comparison Bam.py @ 11:d05236b15f81 draft

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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 3233451a3bd6
comparison
equal deleted inserted replaced
10:acc233161f50 11:d05236b15f81
22 22
23 self.input_bam_false_path = input_bam_false_path 23 self.input_bam_false_path = input_bam_false_path
24 24
25 self.data_bam = data_bam 25 self.data_bam = data_bam
26 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension 26 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
27 self.name_bam = self.data_bam["name"] + ".bam" 27 if ".bam" not in self.data_bam["name"]:
28 self.name_bam = self.data_bam["name"] + ".bam"
29 else:
30 self.name_bam = self.data_bam["name"]
31
28 self.priority = self.data_bam["order_index"] 32 self.priority = self.data_bam["order_index"]
29 self.index_bam = self.data_bam["index"] 33 self.index_bam = self.data_bam["index"]
30 34
31 print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam) 35 #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
32 36
33 # First: Add the bam file 37 # First: Add the bam file
34 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html) 38 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
35 39
36 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam) 40 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
40 name_index_bam = self.name_bam + ".bai" 44 name_index_bam = self.name_bam + ".bai"
41 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam) 45 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
42 shutil.copyfile(self.index_bam, bam_index_file_path) 46 shutil.copyfile(self.index_bam, bam_index_file_path)
43 47
44 # Create the Track Object 48 # Create the Track Object
45 dataURL = "tracks/%s" % self.name_bam 49 self.createTrack(file_path=self.name_bam,
50 track_name=self.name_bam,
51 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
52 track_file=bam_index_file_path)
53 #
54 # dataURL = "tracks/%s" % self.name_bam
55 #
56 # trackDb = TrackDb(
57 # trackName=self.name_bam,
58 # longLabel=self.name_bam,
59 # shortLabel=self.getShortName( self.name_bam ),
60 # trackDataURL=dataURL,
61 # trackType='bam',
62 # visibility='pack',
63 # priority=self.priority,
64 # )
65 #
66 # # Return the Bam Track Object
67 # self.track = Track(
68 # trackFile=bam_index_file_path,
69 # trackDb=trackDb,
70 # )
46 71
47 trackDb = TrackDb( 72 print("- Bam %s created" % self.name_bam)
48 trackName=self.name_bam, 73 #print("- %s created in %s" % (self.name_bam, bam_file_path))
49 longLabel=self.name_bam, 74 #print("- %s created in %s" % (self.index_bam, bam_index_file_path))
50 shortLabel=self.getShortName( self.name_bam ),
51 trackDataURL=dataURL,
52 trackType='bam',
53 visibility='pack',
54 priority=self.priority,
55 )
56
57 # Return the Bam Track Object
58 self.track = Track(
59 trackFile=bam_index_file_path,
60 trackDb=trackDb,
61 )
62
63 print("- %s created in %s" % (self.name_bam, bam_file_path))
64 print("- %s created in %s" % (self.index_bam, bam_index_file_path))