Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.py @ 17:c02720d1afee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children 2677f1899aa8
comparison
equal deleted inserted replaced
16:3233451a3bd6 17:c02720d1afee
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 self.track_color = data_gff3["track_color"]
23 # TODO: Think about how to avoid repetition of the group_name everywhere
24 self.group_name = data_gff3["group_name"]
23 25
24 # TODO: See if we need these temporary files as part of the generated files 26 # TODO: See if we need these temporary files as part of the generated files
25 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 27 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
26 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") 28 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
27 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred") 29 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
57 track_name=trackName, 59 track_name=trackName,
58 long_label=self.name_gff3, 60 long_label=self.name_gff3,
59 track_type='bigGenePred', visibility='dense', 61 track_type='bigGenePred', visibility='dense',
60 priority=self.priority, 62 priority=self.priority,
61 track_file=myBigBedFilePath, 63 track_file=myBigBedFilePath,
62 track_color=self.track_color) 64 track_color=self.track_color,
65 group_name=self.group_name)
63 66
64 print("- Gff3 %s created" % self.name_gff3) 67 print("- Gff3 %s created" % self.name_gff3)