Mercurial > repos > rmarenco > hubarchivecreator

comparison Psl.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 c02720d1afee
children df42241d3731
comparison
equal deleted inserted replaced
22:7ddf651457df 23:2677f1899aa8
17 self.name_psl = data_psl["name"] 17 self.name_psl = data_psl["name"]
18 self.priority = data_psl["order_index"] 18 self.priority = data_psl["order_index"]
19 self.track_color = data_psl["track_color"] 19 self.track_color = data_psl["track_color"]
20 # TODO: Think about how to avoid repetition of the group_name everywhere 20 # TODO: Think about how to avoid repetition of the group_name everywhere
21 self.group_name = data_psl["group_name"] 21 self.group_name = data_psl["group_name"]
22 22 if data_psl["long_label"]:
23 self.long_label = data_psl["long_label"]
24 else:
25 self.long_label = self.name_psl
23 # Temporary files 26 # Temporary files
24 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') 27 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
25 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') 28 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
26 29
27 # Get the bed12+12 with pslToBigPsl 30 # Get the bed12+12 with pslToBigPsl
48 tab=True) 51 tab=True)
49 52
50 # Create the Track Object 53 # Create the Track Object
51 self.createTrack(file_path=trackName, 54 self.createTrack(file_path=trackName,
52 track_name=trackName, 55 track_name=trackName,
53 long_label=self.name_psl, 56 long_label=self.long_label,
54 track_type='bigPsl', visibility='dense', 57 track_type='bigPsl', visibility='dense',
55 priority=self.priority, 58 priority=self.priority,
56 track_file=my_big_psl_file_path, 59 track_file=my_big_psl_file_path,
57 track_color=self.track_color, 60 track_color=self.track_color,
58 group_name=self.group_name) 61 group_name=self.group_name)