Mercurial > repos > rmarenco > hubarchivecreator
comparison BedSimpleRepeats.py @ 17:c02720d1afee draft
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 |
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| 16:3233451a3bd6 | 17:c02720d1afee |
|---|---|
| 16 | 16 |
| 17 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path | 17 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path |
| 18 self.name_bed_simple_repeats = data_bed_simple_repeats["name"] | 18 self.name_bed_simple_repeats = data_bed_simple_repeats["name"] |
| 19 self.priority = data_bed_simple_repeats["order_index"] | 19 self.priority = data_bed_simple_repeats["order_index"] |
| 20 self.track_color = data_bed_simple_repeats["track_color"] | 20 self.track_color = data_bed_simple_repeats["track_color"] |
| 21 # TODO: Think about how to avoid repetition of the group_name everywhere | |
| 22 self.group_name = data_bed_simple_repeats["group_name"] | |
| 21 | 23 |
| 22 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | 24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") |
| 23 | 25 |
| 24 # Sort processing | 26 # Sort processing |
| 25 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) | 27 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) |
| 42 self.createTrack(file_path=trackName, | 44 self.createTrack(file_path=trackName, |
| 43 track_name=trackName, | 45 track_name=trackName, |
| 44 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', | 46 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', |
| 45 priority=self.priority, | 47 priority=self.priority, |
| 46 track_file=myBigBedFilePath, | 48 track_file=myBigBedFilePath, |
| 47 track_color=self.track_color) | 49 track_color=self.track_color, |
| 50 group_name=self.group_name) | |
| 48 | 51 |
| 49 # dataURL = "tracks/%s" % trackName | 52 # dataURL = "tracks/%s" % trackName |
| 50 # | 53 # |
| 51 # trackDb = TrackDb( | 54 # trackDb = TrackDb( |
| 52 # trackName=trackName, | 55 # trackName=trackName, |