Mercurial > repos > yating-l > hubarchivecreator

comparison bigPsl.py @ 51:364b8db8de17 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 16:51:03 -0400
parents d5781fe7b782
children c66803bff0cc
comparison
equal deleted inserted replaced
50:47dc3e7470dd 51:364b8db8de17
1 #!/usr/bin/python 1 #!/usr/bin/python
2 2
3 import os 3 import os
4 import tempfile 4 import tempfile
5 import string
5 6
6 from Datatype import Datatype 7 from Datatype import Datatype
7 from Track import Track 8 from Track import Track
8 from TrackDb import TrackDb 9 from TrackDb import TrackDb
9 from util import subtools 10 from util import subtools
27 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) 28 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
28 29
29 # bedToBigBed processing 30 # bedToBigBed processing
30 # TODO: Change the name of the bb, to tool + genome + .bb 31 # TODO: Change the name of the bb, to tool + genome + .bb
31 trackName = "".join( ( self.name_bigpsl, '.bb' ) ) 32 trackName = "".join( ( self.name_bigpsl, '.bb' ) )
33
32 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
33 35
34 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') 36 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
35 37
36 with open(myBigBedFilePath, 'w') as bigBedFile: 38 with open(myBigBedFilePath, 'w') as bigBedFile:
39 bigBedFile.name, 41 bigBedFile.name,
40 typeOption='bed12+12', 42 typeOption='bed12+12',
41 tab='True', 43 tab='True',
42 autoSql=auto_sql_option) 44 autoSql=auto_sql_option)
43 45
44 # Create the Track Object
45 self.createTrack(file_path=trackName, 46 self.createTrack(file_path=trackName,
46 track_name=trackName, 47 track_name=trackName,
47 long_label=self.name_bigpsl, track_type='bigBed 12 +', visibility='dense', 48 long_label=self.name_bigpsl, track_type='bigPsl', visibility='dense',
48 priority=self.priority, 49 priority=self.priority,
49 track_file=myBigBedFilePath, 50 track_file=myBigBedFilePath,
50 track_color=self.track_color, 51 track_color=self.track_color,
51 group_name=self.group_name) 52 group_name=self.group_name)
53
52 54
53 # dataURL = "tracks/%s" % trackName 55 # dataURL = "tracks/%s" % trackName
54 # 56 #
55 # trackDb = TrackDb( 57 # trackDb = TrackDb(
56 # trackName=trackName, 58 # trackName=trackName,