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comparison Bed.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
3 import os
4 import tempfile
5
6 # Internal dependencies
7 from Datatype import Datatype
8 from Track import Track
9 from TrackDb import TrackDb
10 from util import subtools
11
12
13 class Bed( Datatype ):
14 def __init__( self, inputBedGeneric, data_bed_generic):
15 super(Bed, self).__init__()
16
17 self.track = None
18
19 self.inputBedGeneric = inputBedGeneric
20
21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
22
23 self.data_bed_generic = data_bed_generic
24 self.name_bed_generic = self.data_bed_generic["name"]
25 self.priority = self.data_bed_generic["order_index"]
26 self.track_color = self.data_bed_generic["track_color"]
27 # TODO: Think about how to avoid repetition of the group_name everywhere
28 self.group_name = self.data_bed_generic["group_name"]
29
30
31 # Sort processing
32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
33
34 # bedToBigBed processing
35 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
36 trackName = "".join( ( self.name_bed_generic, ".bb") )
37
38 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
39 with open(myBigBedFilePath, 'w') as self.bigBedFile:
40 subtools.bedToBigBed(self.sortedBedFile.name,
41 self.chromSizesFile.name,
42 self.bigBedFile.name)
43
44 # Create the Track Object
45 self.createTrack(file_path=trackName,
46 track_name=trackName,
47 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
48 priority=self.priority,
49 track_file=myBigBedFilePath,
50 track_color=self.track_color,
51 group_name=self.group_name)
52
53 # dataURL = "tracks/%s" % trackName
54 #
55 # trackDb = TrackDb(
56 # trackName=trackName,
57 # longLabel=self.name_bed_generic,
58 # shortLabel=self.getShortName(self.name_bed_generic),
59 # trackDataURL=dataURL,
60 # trackType='bigBed',
61 # visibility='dense',
62 # thickDrawItem='on',
63 # priority=self.priority,
64 # )
65 #
66 # # Return the BigBed track
67 # self.track = Track(
68 # trackFile=myBigBedFilePath,
69 # trackDb=trackDb,
70 # )
71
72 print("- Bed %s created" % self.name_bed_generic)
73 #print("- %s created in %s" % (trackName, myBigBedFilePath))