Mercurial > repos > rmarenco > hubarchivecreator
comparison Bed.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 |
|---|---|
| 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 self.track_color = self.data_bed_generic["track_color"] |
| 27 # TODO: Think about how to avoid repetition of the group_name everywhere | 27 # TODO: Think about how to avoid repetition of the group_name everywhere |
| 28 self.group_name = self.data_bed_generic["group_name"] | 28 self.group_name = self.data_bed_generic["group_name"] |
| 29 | 29 if self.data_bed_generic["long_label"]: |
| 30 self.long_label = self.data_bed_generic["long_label"] | |
| 31 else: | |
| 32 self.long_label = self.name_bed_generic | |
| 30 | 33 |
| 31 # Sort processing | 34 # Sort processing |
| 32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) | 35 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) |
| 33 | 36 |
| 34 # bedToBigBed processing | 37 # bedToBigBed processing |
| 42 self.bigBedFile.name) | 45 self.bigBedFile.name) |
| 43 | 46 |
| 44 # Create the Track Object | 47 # Create the Track Object |
| 45 self.createTrack(file_path=trackName, | 48 self.createTrack(file_path=trackName, |
| 46 track_name=trackName, | 49 track_name=trackName, |
| 47 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', | 50 long_label=self.long_label, track_type='bigBed', visibility='dense', |
| 48 priority=self.priority, | 51 priority=self.priority, |
| 49 track_file=myBigBedFilePath, | 52 track_file=myBigBedFilePath, |
| 50 track_color=self.track_color, | 53 track_color=self.track_color, |
| 51 group_name=self.group_name) | 54 group_name=self.group_name) |
| 52 | 55 |