Mercurial > repos > rmarenco > hubarchivecreator

comparison Bam.py @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children 884ee2a71680
comparison
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16:3233451a3bd6 17:c02720d1afee
30 else: 30 else:
31 self.name_bam = self.data_bam["name"] 31 self.name_bam = self.data_bam["name"]
32 32
33 self.priority = self.data_bam["order_index"] 33 self.priority = self.data_bam["order_index"]
34 self.index_bam = self.data_bam["index"] 34 self.index_bam = self.data_bam["index"]
35 # TODO: Think about how to avoir repetition of the color treatment 35 # TODO: Think about how to avoid repetition of the color treatment
36 self.track_color = self.data_bam["track_color"] 36 self.track_color = self.data_bam["track_color"]
37 37
38 logging.debug("Color of bam: {0}".format(self.track_color)) 38 # TODO: Think about how to avoid repetition of the group_name everywhere
39 39 self.group_name = self.data_bam["group_name"]
40 #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
41 40
42 # First: Add the bam file 41 # First: Add the bam file
43 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html) 42 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
44 43
45 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam) 44 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
53 # Create the Track Object 52 # Create the Track Object
54 self.createTrack(file_path=self.name_bam, 53 self.createTrack(file_path=self.name_bam,
55 track_name=self.name_bam, 54 track_name=self.name_bam,
56 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority, 55 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
57 track_file=bam_index_file_path, 56 track_file=bam_index_file_path,
58 track_color=self.track_color) 57 track_color=self.track_color,
58 group_name=self.group_name
59 )
59 # 60 #
60 # dataURL = "tracks/%s" % self.name_bam 61 # dataURL = "tracks/%s" % self.name_bam
61 # 62 #
62 # trackDb = TrackDb( 63 # trackDb = TrackDb(
63 # trackName=self.name_bam, 64 # trackName=self.name_bam,