Mercurial > repos > yating-l > hubarchivecreator

comparison BedSpliceJunctions.py @ 57:b39dd0b5a166 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
author yating-l
date Fri, 30 Jun 2017 14:49:14 -0400
parents c66803bff0cc
children a0fc8379223c
comparison
equal deleted inserted replaced
56:04cc7c2e7b47 57:b39dd0b5a166
18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"] 18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
19 self.priority = data_bed_splice_junctions["order_index"] 19 self.priority = data_bed_splice_junctions["order_index"]
20 self.track_color = data_bed_splice_junctions["track_color"] 20 self.track_color = data_bed_splice_junctions["track_color"]
21 # TODO: Think about how to avoid repetition of the group_name everywhere 21 # TODO: Think about how to avoid repetition of the group_name everywhere
22 self.group_name = data_bed_splice_junctions["group_name"] 22 self.group_name = data_bed_splice_junctions["group_name"]
23 self.database = data_bed_splice_junctions["database"]
23 if data_bed_splice_junctions["long_label"]: 24 if data_bed_splice_junctions["long_label"]:
24 self.long_label = data_bed_splice_junctions["long_label"] 25 self.long_label = data_bed_splice_junctions["long_label"]
25 else: 26 else:
26 self.long_label = self.name_bed_splice_junctions 27 self.long_label = self.name_bed_splice_junctions
27 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 28 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
39 with open(myBigBedFilePath, 'w') as bigBedFile: 40 with open(myBigBedFilePath, 'w') as bigBedFile:
40 subtools.bedToBigBed(sortedBedFile.name, 41 subtools.bedToBigBed(sortedBedFile.name,
41 self.chromSizesFile.name, 42 self.chromSizesFile.name,
42 bigBedFile.name, 43 bigBedFile.name,
43 typeOption='bed12+1', 44 typeOption='bed12+1',
44 autoSql=auto_sql_option) 45 autoSql=auto_sql_option
46 )
45 47
46 # Create the Track Object 48 # Create the Track Object
47 self.createTrack(file_path=trackName, 49 self.createTrack(file_path=trackName,
48 track_name=trackName, 50 track_name=trackName,
49 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', 51 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
50 priority=self.priority, 52 priority=self.priority,
51 track_file=myBigBedFilePath, 53 track_file=myBigBedFilePath,
52 track_color=self.track_color, 54 track_color=self.track_color,
53 group_name=self.group_name) 55 group_name=self.group_name,
56 database=self.database)
54 57
55 # dataURL = "tracks/%s" % trackName 58 # dataURL = "tracks/%s" % trackName
56 # 59 #
57 # trackDb = TrackDb( 60 # trackDb = TrackDb(
58 # trackName=trackName, 61 # trackName=trackName,