Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.py @ 16:3233451a3bd6 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
parents 25809f699cb3
children c02720d1afee
comparison
equal deleted inserted replaced
15:2a45cd656e8e 16:3233451a3bd6
17 self.track = None 17 self.track = None
18 18
19 self.input_Gff3_false_path = input_Gff3_false_path 19 self.input_Gff3_false_path = input_Gff3_false_path
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 23
23 # TODO: See if we need these temporary files as part of the generated files 24 # TODO: See if we need these temporary files as part of the generated files
24 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 25 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
25 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") 26 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
26 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") 27 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
55 self.createTrack(file_path=trackName, 56 self.createTrack(file_path=trackName,
56 track_name=trackName, 57 track_name=trackName,
57 long_label=self.name_gff3, 58 long_label=self.name_gff3,
58 track_type='bigGenePred', visibility='dense', 59 track_type='bigGenePred', visibility='dense',
59 priority=self.priority, 60 priority=self.priority,
60 track_file=myBigBedFilePath) 61 track_file=myBigBedFilePath,
62 track_color=self.track_color)
61 63
62 print("- Gff3 %s created" % self.name_gff3) 64 print("- Gff3 %s created" % self.name_gff3)