Mercurial > repos > rmarenco > hubarchivecreator

annotate BedBlastAlignments.py @ 21:884ee2a71680 draft

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