Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.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
20 self.name_gff3 = data_gff3["name"] 20 self.name_gff3 = data_gff3["name"]
21 self.priority = data_gff3["order_index"] 21 self.priority = data_gff3["order_index"]
22 self.track_color = data_gff3["track_color"] 22 self.track_color = data_gff3["track_color"]
23 # TODO: Think about how to avoid repetition of the group_name everywhere 23 # TODO: Think about how to avoid repetition of the group_name everywhere
24 self.group_name = data_gff3["group_name"] 24 self.group_name = data_gff3["group_name"]
25 25 if data_gff3["long_label"]:
26 self.long_label = data_gff3["long_label"]
27 else:
28 self.long_label = self.name_gff3
26 # TODO: See if we need these temporary files as part of the generated files 29 # TODO: See if we need these temporary files as part of the generated files
27 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 30 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
28 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") 31 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
29 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") 32 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
30 33
55 tab=True) 58 tab=True)
56 59
57 # Create the Track Object 60 # Create the Track Object
58 self.createTrack(file_path=trackName, 61 self.createTrack(file_path=trackName,
59 track_name=trackName, 62 track_name=trackName,
60 long_label=self.name_gff3, 63 long_label=self.long_label,
61 track_type='bigGenePred', visibility='dense', 64 track_type='bigGenePred', visibility='dense',
62 priority=self.priority, 65 priority=self.priority,
63 track_file=myBigBedFilePath, 66 track_file=myBigBedFilePath,
64 track_color=self.track_color, 67 track_color=self.track_color,
65 group_name=self.group_name) 68 group_name=self.group_name)