Mercurial > repos > rmarenco > hubarchivecreator

comparison BedBlastAlignments.py @ 21:884ee2a71680 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 15:05:33 -0400
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children 2677f1899aa8
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20:40469b265ddb 21:884ee2a71680
1 #!/usr/bin/python
2
3 import os
4 import tempfile
5 import string
6
7 from Datatype import Datatype
8 from Track import Track
9 from TrackDb import TrackDb
10 from util import subtools
11
12
13 class BedBlastAlignments( Datatype ):
14 def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments):
15
16 super(BedBlastAlignments, self).__init__()
17
18 self.input_bed_blast_alignments_false_path = input_bed_blast_alignments_false_path
19 self.name_bed_blast_alignments = data_bed_blast_alignments["name"]
20 self.priority = data_bed_blast_alignments["order_index"]
21 self.track_color = data_bed_blast_alignments["track_color"]
22 # TODO: Think about how to avoid repetition of the group_name everywhere
23 self.group_name = data_bed_blast_alignments["group_name"]
24
25 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
26
27 # Sort processing
28 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
29
30 # bedToBigBed processing
31 # TODO: Change the name of the bb, to tool + genome + .bb
32 trackName = "".join( ( self.name_bed_blast_alignments, '.bb' ) )
33
34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
35
36 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
37
38 with open(myBigBedFilePath, 'w') as bigBedFile:
39 subtools.bedToBigBed(self.input_bed_blast_alignments_false_path,
40 self.chromSizesFile.name,
41 bigBedFile.name,
42 typeOption='bed12+12',
43 tab='True',
44 autoSql=auto_sql_option)
45
46 self.createTrack(file_path=trackName,
47 track_name=trackName,
48 long_label=self.name_bed_blast_alignments, track_type='bigBed 12 +', visibility='dense',
49 priority=self.priority,
50 track_file=myBigBedFilePath,
51 track_color=self.track_color,
52 group_name=self.group_name)
53
54
55 # dataURL = "tracks/%s" % trackName
56 #
57 # trackDb = TrackDb(
58 # trackName=trackName,
59 # longLabel=self.name_bed_simple_repeats,
60 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
61 # trackDataURL=dataURL,
62 # trackType='bigBed 4 +',
63 # visibility='dense',
64 # priority=self.priority,
65 # )
66 #
67 # self.track = Track(
68 # trackFile=myBigBedFilePath,
69 # trackDb=trackDb,
70 # )
71
72 print("- Bed Blast alignments %s created" % self.name_bed_blast_alignments)
73 #print("- %s created in %s" % (trackName, myBigBedFilePath))