Mercurial > repos > yating-l > hubarchivecreator
comparison Gff3.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 |
|---|---|
| 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) |