Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSpliceJunctions.py @ 23:2677f1899aa8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author yating-l
date Tue, 09 May 2017 15:42:43 -0400
parents 40469b265ddb
children df42241d3731
comparison
equal deleted inserted replaced
22:7ddf651457df 23:2677f1899aa8
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 23 if data_bed_splice_junctions["long_label"]:
24 self.long_label = data_bed_splice_junctions["long_label"]
25 else:
26 self.long_label = self.name_bed_splice_junctions
24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 27 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
25 28
26 # Sort processing 29 # Sort processing
27 subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name) 30 subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
28 31
41 autoSql=auto_sql_option) 44 autoSql=auto_sql_option)
42 45
43 # Create the Track Object 46 # Create the Track Object
44 self.createTrack(file_path=trackName, 47 self.createTrack(file_path=trackName,
45 track_name=trackName, 48 track_name=trackName,
46 long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense', 49 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
47 priority=self.priority, 50 priority=self.priority,
48 track_file=myBigBedFilePath, 51 track_file=myBigBedFilePath,
49 track_color=self.track_color, 52 track_color=self.track_color,
50 group_name=self.group_name) 53 group_name=self.group_name)
51 54