Mercurial > repos > rmarenco > hubarchivecreator

annotate BedBlastAlignments.py @ 26:df42241d3731 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 c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 2677f1899aa8
children
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"]
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
24 self.database = data_bed_blast_alignments["database"]
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 21
diff changeset
25 if data_bed_blast_alignments["long_label"]:
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 21
diff changeset
26 self.long_label = data_bed_blast_alignments["long_label"]
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 21
diff changeset
27 else:
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 21
diff changeset
28 self.long_label = self.name_bed_blast_alignments
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
29 #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
30
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
31 # Sort processing
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
32 #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
33
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
34 # bedToBigBed processing
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
35 # 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
36 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
37
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
38 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
39
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
40 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
41
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
42 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
43 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
44 self.chromSizesFile.name,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
45 bigBedFile.name,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
46 typeOption='bed12+12',
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
47 tab='True',
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
48 autoSql=auto_sql_option,
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
49 extraIndex='name')
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
50
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
51 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
52 track_name=trackName,
23
2677f1899aa8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents: 21
diff changeset
53 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
54 priority=self.priority,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
55 track_file=myBigBedFilePath,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
56 track_color=self.track_color,
26
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
57 group_name=self.group_name,
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
58 database=self.database
df42241d3731 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents: 23
diff changeset
59 )
21
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
60
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
61
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
62 # dataURL = "tracks/%s" % trackName
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
63 #
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
64 # trackDb = TrackDb(
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
65 # trackName=trackName,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
66 # 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
67 # 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
68 # trackDataURL=dataURL,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
69 # trackType='bigBed 4 +',
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
70 # visibility='dense',
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
71 # priority=self.priority,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
72 # )
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
73 #
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
74 # self.track = Track(
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
75 # trackFile=myBigBedFilePath,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
76 # trackDb=trackDb,
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
77 # )
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
78
884ee2a71680 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents:
diff changeset
79 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
80 #print("- %s created in %s" % (trackName, myBigBedFilePath))