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comparison Bam.py @ 0:f493979f1408 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 12:13:04 -0500
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-1:000000000000 0:f493979f1408
1 #!/usr/bin/python
2 # -*- coding: utf8 -*-
3
4 """
5 Class to handle Bam files to UCSC TrackHub
6 """
7
8 import logging
9 import os
10 import shutil
11
12 from Datatype import Datatype
13 from Track import Track
14 from TrackDb import TrackDb
15 from util import subtools
16
17
18 class Bam( Datatype ):
19 def __init__(self, input_bam_false_path, data_bam):
20 super(Bam, self).__init__()
21
22 self.track = None
23
24 self.input_bam_false_path = input_bam_false_path
25
26 self.data_bam = data_bam
27 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
28 if ".bam" not in self.data_bam["name"]:
29 self.name_bam = self.data_bam["name"] + ".bam"
30 else:
31 self.name_bam = self.data_bam["name"]
32
33 self.priority = self.data_bam["order_index"]
34 self.index_bam = self.data_bam["index"]
35 # TODO: Think about how to avoid repetition of the color treatment
36 self.track_color = self.data_bam["track_color"]
37
38 # TODO: Think about how to avoid repetition of the group_name everywhere
39 self.group_name = self.data_bam["group_name"]
40
41 # First: Add the bam file
42 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
43
44 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
45 shutil.copyfile(self.input_bam_false_path, bam_file_path)
46
47 # Create and add the bam index file to the same folder
48 name_index_bam = self.name_bam + ".bai"
49 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
50 shutil.copyfile(self.index_bam, bam_index_file_path)
51
52 # Create the Track Object
53 self.createTrack(file_path=self.name_bam,
54 track_name=self.name_bam,
55 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
56 track_file=bam_index_file_path,
57 track_color=self.track_color,
58 group_name=self.group_name
59 )
60 #
61 # dataURL = "tracks/%s" % self.name_bam
62 #
63 # trackDb = TrackDb(
64 # trackName=self.name_bam,
65 # longLabel=self.name_bam,
66 # shortLabel=self.getShortName( self.name_bam ),
67 # trackDataURL=dataURL,
68 # trackType='bam',
69 # visibility='pack',
70 # priority=self.priority,
71 # )
72 #
73 # # Return the Bam Track Object
74 # self.track = Track(
75 # trackFile=bam_index_file_path,
76 # trackDb=trackDb,
77 # )
78
79 print("- Bam %s created" % self.name_bam)
80 #print("- %s created in %s" % (self.name_bam, bam_file_path))
81 #print("- %s created in %s" % (self.index_bam, bam_index_file_path))