Mercurial > repos > rmarenco > hubarchivecreator

comparison Bam.py @ 16:3233451a3bd6 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
parents d05236b15f81
children c02720d1afee
comparison
equal deleted inserted replaced
15:2a45cd656e8e 16:3233451a3bd6
3 3
4 """ 4 """
5 Class to handle Bam files to UCSC TrackHub 5 Class to handle Bam files to UCSC TrackHub
6 """ 6 """
7 7
8 import logging
8 import os 9 import os
9 import shutil 10 import shutil
10 11
11 from Datatype import Datatype 12 from Datatype import Datatype
12 from Track import Track 13 from Track import Track
29 else: 30 else:
30 self.name_bam = self.data_bam["name"] 31 self.name_bam = self.data_bam["name"]
31 32
32 self.priority = self.data_bam["order_index"] 33 self.priority = self.data_bam["order_index"]
33 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
36 self.track_color = self.data_bam["track_color"]
37
38 logging.debug("Color of bam: {0}".format(self.track_color))
34 39
35 #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam) 40 #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
36 41
37 # First: Add the bam file 42 # First: Add the bam file
38 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html) 43 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
47 52
48 # Create the Track Object 53 # Create the Track Object
49 self.createTrack(file_path=self.name_bam, 54 self.createTrack(file_path=self.name_bam,
50 track_name=self.name_bam, 55 track_name=self.name_bam,
51 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority, 56 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
52 track_file=bam_index_file_path) 57 track_file=bam_index_file_path,
58 track_color=self.track_color)
53 # 59 #
54 # dataURL = "tracks/%s" % self.name_bam 60 # dataURL = "tracks/%s" % self.name_bam
55 # 61 #
56 # trackDb = TrackDb( 62 # trackDb = TrackDb(
57 # trackName=self.name_bam, 63 # trackName=self.name_bam,