Mercurial > repos > rmarenco > hubarchivecreator
comparison Psl.py @ 23:2677f1899aa8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
| author | yating-l |
|---|---|
| date | Tue, 09 May 2017 15:42:43 -0400 |
| parents | c02720d1afee |
| children | df42241d3731 |
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| 22:7ddf651457df | 23:2677f1899aa8 |
|---|---|
| 17 self.name_psl = data_psl["name"] | 17 self.name_psl = data_psl["name"] |
| 18 self.priority = data_psl["order_index"] | 18 self.priority = data_psl["order_index"] |
| 19 self.track_color = data_psl["track_color"] | 19 self.track_color = data_psl["track_color"] |
| 20 # TODO: Think about how to avoid repetition of the group_name everywhere | 20 # TODO: Think about how to avoid repetition of the group_name everywhere |
| 21 self.group_name = data_psl["group_name"] | 21 self.group_name = data_psl["group_name"] |
| 22 | 22 if data_psl["long_label"]: |
| 23 self.long_label = data_psl["long_label"] | |
| 24 else: | |
| 25 self.long_label = self.name_psl | |
| 23 # Temporary files | 26 # Temporary files |
| 24 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') | 27 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') |
| 25 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') | 28 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') |
| 26 | 29 |
| 27 # Get the bed12+12 with pslToBigPsl | 30 # Get the bed12+12 with pslToBigPsl |
| 48 tab=True) | 51 tab=True) |
| 49 | 52 |
| 50 # Create the Track Object | 53 # Create the Track Object |
| 51 self.createTrack(file_path=trackName, | 54 self.createTrack(file_path=trackName, |
| 52 track_name=trackName, | 55 track_name=trackName, |
| 53 long_label=self.name_psl, | 56 long_label=self.long_label, |
| 54 track_type='bigPsl', visibility='dense', | 57 track_type='bigPsl', visibility='dense', |
| 55 priority=self.priority, | 58 priority=self.priority, |
| 56 track_file=my_big_psl_file_path, | 59 track_file=my_big_psl_file_path, |
| 57 track_color=self.track_color, | 60 track_color=self.track_color, |
| 58 group_name=self.group_name) | 61 group_name=self.group_name) |