Mercurial > repos > yating-l > hubarchivecreator

comparison Gtf.py @ 57:b39dd0b5a166 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
author yating-l
date Fri, 30 Jun 2017 14:49:14 -0400
parents c66803bff0cc
children a0fc8379223c
comparison
equal deleted inserted replaced
56:04cc7c2e7b47 57:b39dd0b5a166
26 self.name_gtf = data_gtf["name"] 26 self.name_gtf = data_gtf["name"]
27 self.priority = data_gtf["order_index"] 27 self.priority = data_gtf["order_index"]
28 self.track_color = data_gtf["track_color"] 28 self.track_color = data_gtf["track_color"]
29 # TODO: Think about how to avoid repetition of the group_name everywhere 29 # TODO: Think about how to avoid repetition of the group_name everywhere
30 self.group_name = data_gtf["group_name"] 30 self.group_name = data_gtf["group_name"]
31 self.database = data_gtf["database"]
31 if data_gtf["long_label"]: 32 if data_gtf["long_label"]:
32 self.long_label = data_gtf["long_label"] 33 self.long_label = data_gtf["long_label"]
33 else: 34 else:
34 self.long_label = self.name_gtf 35 self.long_label = self.name_gtf
35 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) 36 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
74 track_name=trackName, 75 track_name=trackName,
75 long_label=self.long_label, track_type='bigGenePred', 76 long_label=self.long_label, track_type='bigGenePred',
76 visibility='dense', priority=self.priority, 77 visibility='dense', priority=self.priority,
77 track_file=myBigBedFilePath, 78 track_file=myBigBedFilePath,
78 track_color=self.track_color, 79 track_color=self.track_color,
79 group_name=self.group_name) 80 group_name=self.group_name,
81 database=self.database)
80 82
81 # TODO: Use Logging instead of print 83 # TODO: Use Logging instead of print
82 if modified_gtf.is_modified: 84 if modified_gtf.is_modified:
83 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues." 85 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues."
84 % self.name_gtf) 86 % self.name_gtf)