Mercurial > repos > rmarenco > hubarchivecreator
comparison Bed.py @ 16:3233451a3bd6 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
| author | rmarenco |
|---|---|
| date | Sun, 25 Sep 2016 11:25:38 -0400 |
| parents | 25809f699cb3 |
| children | c02720d1afee |
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| 15:2a45cd656e8e | 16:3233451a3bd6 |
|---|---|
| 21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | 21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") |
| 22 | 22 |
| 23 self.data_bed_generic = data_bed_generic | 23 self.data_bed_generic = data_bed_generic |
| 24 self.name_bed_generic = self.data_bed_generic["name"] | 24 self.name_bed_generic = self.data_bed_generic["name"] |
| 25 self.priority = self.data_bed_generic["order_index"] | 25 self.priority = self.data_bed_generic["order_index"] |
| 26 self.track_color = self.data_bed_generic["track_color"] | |
| 26 | 27 |
| 27 # Sort processing | 28 # Sort processing |
| 28 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) | 29 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) |
| 29 | 30 |
| 30 # bedToBigBed processing | 31 # bedToBigBed processing |
| 40 # Create the Track Object | 41 # Create the Track Object |
| 41 self.createTrack(file_path=trackName, | 42 self.createTrack(file_path=trackName, |
| 42 track_name=trackName, | 43 track_name=trackName, |
| 43 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', | 44 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', |
| 44 priority=self.priority, | 45 priority=self.priority, |
| 45 track_file=myBigBedFilePath) | 46 track_file=myBigBedFilePath, |
| 47 track_color=self.track_color) | |
| 46 | 48 |
| 47 # dataURL = "tracks/%s" % trackName | 49 # dataURL = "tracks/%s" % trackName |
| 48 # | 50 # |
| 49 # trackDb = TrackDb( | 51 # trackDb = TrackDb( |
| 50 # trackName=trackName, | 52 # trackName=trackName, |