Mercurial > repos > yating-l > hubarchivecreator
comparison BedSpliceJunctions.py @ 57:b39dd0b5a166 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
| author | yating-l |
|---|---|
| date | Fri, 30 Jun 2017 14:49:14 -0400 |
| parents | c66803bff0cc |
| children | a0fc8379223c |
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| 56:04cc7c2e7b47 | 57:b39dd0b5a166 |
|---|---|
| 18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"] | 18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"] |
| 19 self.priority = data_bed_splice_junctions["order_index"] | 19 self.priority = data_bed_splice_junctions["order_index"] |
| 20 self.track_color = data_bed_splice_junctions["track_color"] | 20 self.track_color = data_bed_splice_junctions["track_color"] |
| 21 # TODO: Think about how to avoid repetition of the group_name everywhere | 21 # TODO: Think about how to avoid repetition of the group_name everywhere |
| 22 self.group_name = data_bed_splice_junctions["group_name"] | 22 self.group_name = data_bed_splice_junctions["group_name"] |
| 23 self.database = data_bed_splice_junctions["database"] | |
| 23 if data_bed_splice_junctions["long_label"]: | 24 if data_bed_splice_junctions["long_label"]: |
| 24 self.long_label = data_bed_splice_junctions["long_label"] | 25 self.long_label = data_bed_splice_junctions["long_label"] |
| 25 else: | 26 else: |
| 26 self.long_label = self.name_bed_splice_junctions | 27 self.long_label = self.name_bed_splice_junctions |
| 27 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | 28 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") |
| 39 with open(myBigBedFilePath, 'w') as bigBedFile: | 40 with open(myBigBedFilePath, 'w') as bigBedFile: |
| 40 subtools.bedToBigBed(sortedBedFile.name, | 41 subtools.bedToBigBed(sortedBedFile.name, |
| 41 self.chromSizesFile.name, | 42 self.chromSizesFile.name, |
| 42 bigBedFile.name, | 43 bigBedFile.name, |
| 43 typeOption='bed12+1', | 44 typeOption='bed12+1', |
| 44 autoSql=auto_sql_option) | 45 autoSql=auto_sql_option |
| 46 ) | |
| 45 | 47 |
| 46 # Create the Track Object | 48 # Create the Track Object |
| 47 self.createTrack(file_path=trackName, | 49 self.createTrack(file_path=trackName, |
| 48 track_name=trackName, | 50 track_name=trackName, |
| 49 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', | 51 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', |
| 50 priority=self.priority, | 52 priority=self.priority, |
| 51 track_file=myBigBedFilePath, | 53 track_file=myBigBedFilePath, |
| 52 track_color=self.track_color, | 54 track_color=self.track_color, |
| 53 group_name=self.group_name) | 55 group_name=self.group_name, |
| 56 database=self.database) | |
| 54 | 57 |
| 55 # dataURL = "tracks/%s" % trackName | 58 # dataURL = "tracks/%s" % trackName |
| 56 # | 59 # |
| 57 # trackDb = TrackDb( | 60 # trackDb = TrackDb( |
| 58 # trackName=trackName, | 61 # trackName=trackName, |