Mercurial > repos > yating-l > hubarchivecreator
comparison Gtf.py @ 52:c66803bff0cc draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
| author | yating-l |
|---|---|
| date | Thu, 11 May 2017 17:21:15 -0400 |
| parents | 3e0c61b52a06 |
| children | b39dd0b5a166 |
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| 51:364b8db8de17 | 52:c66803bff0cc |
|---|---|
| 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 | 31 if data_gtf["long_label"]: |
| 32 self.long_label = data_gtf["long_label"] | |
| 33 else: | |
| 34 self.long_label = self.name_gtf | |
| 32 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) | 35 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) |
| 33 | 36 |
| 34 # TODO: See if we need these temporary files as part of the generated files | 37 # TODO: See if we need these temporary files as part of the generated files |
| 35 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") | 38 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") |
| 36 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") | 39 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") |
| 67 | 70 |
| 68 | 71 |
| 69 # Create the Track Object | 72 # Create the Track Object |
| 70 self.createTrack(file_path=trackName, | 73 self.createTrack(file_path=trackName, |
| 71 track_name=trackName, | 74 track_name=trackName, |
| 72 long_label=self.name_gtf, track_type='bigGenePred', | 75 long_label=self.long_label, track_type='bigGenePred', |
| 73 visibility='dense', priority=self.priority, | 76 visibility='dense', priority=self.priority, |
| 74 track_file=myBigBedFilePath, | 77 track_file=myBigBedFilePath, |
| 75 track_color=self.track_color, | 78 track_color=self.track_color, |
| 76 group_name=self.group_name) | 79 group_name=self.group_name) |
| 77 | 80 |