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comparison Bam.py @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children acc233161f50
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0:0f3bc17e5ede 1:fb5e60d4d18a
1 #!/usr/bin/python
2 # -*- coding: utf8 -*-
3
4 """
5 Class to handle Bam files to UCSC TrackHub
6 """
7
8 import os
9 import shutil
10
11 from Datatype import Datatype
12 from Track import Track
13 from TrackDb import TrackDb
14 from util import subtools
15
16
17 class Bam( Datatype ):
18 def __init__( self, input_bam_false_path, data_bam ,
19 inputFastaFile, extra_files_path, tool_directory ):
20 super(Bam, self).__init__( input_fasta_file=inputFastaFile,
21 extra_files_path=extra_files_path,
22 tool_directory=tool_directory,
23 )
24
25 self.track = None
26
27 self.input_bam_false_path = input_bam_false_path
28
29 self.data_bam = data_bam
30 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
31 self.name_bam = self.data_bam["name"] + ".bam"
32 self.priority = self.data_bam["order_index"]
33 self.index_bam = self.data_bam["index"]
34
35 print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
36
37 # First: Add the bam file
38 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
39
40 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
41 shutil.copyfile(self.input_bam_false_path, bam_file_path)
42
43 # Create and add the bam index file to the same folder
44 name_index_bam = self.name_bam + ".bai"
45 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
46 shutil.copyfile(self.index_bam, bam_index_file_path)
47
48 # Create the Track Object
49 dataURL = "tracks/%s" % self.name_bam
50
51 trackDb = TrackDb(
52 trackName=self.name_bam,
53 longLabel=self.name_bam,
54 shortLabel=self.getShortName( self.name_bam ),
55 trackDataURL=dataURL,
56 trackType='bam',
57 visibility='pack',
58 priority=self.priority,
59 )
60
61 # Return the Bam Track Object
62 self.track = Track(
63 trackFile=bam_index_file_path,
64 trackDb=trackDb,
65 )
66
67 print("- %s created in %s" % (self.name_bam, bam_file_path))
68 print("- %s created in %s" % (self.index_bam, bam_index_file_path))