Mercurial > repos > yating-l > hubarchivecreator
comparison BedSimpleRepeats.py @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 12:13:04 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:f493979f1408 |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import tempfile | |
| 5 | |
| 6 from Datatype import Datatype | |
| 7 from Track import Track | |
| 8 from TrackDb import TrackDb | |
| 9 from util import subtools | |
| 10 | |
| 11 | |
| 12 class BedSimpleRepeats( Datatype ): | |
| 13 def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats): | |
| 14 | |
| 15 super(BedSimpleRepeats, self).__init__() | |
| 16 | |
| 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"] | |
| 19 self.priority = data_bed_simple_repeats["order_index"] | |
| 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"] | |
| 23 | |
| 24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | |
| 25 | |
| 26 # Sort processing | |
| 27 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) | |
| 28 | |
| 29 # bedToBigBed processing | |
| 30 # TODO: Change the name of the bb, to tool + genome + .bb | |
| 31 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) ) | |
| 32 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 33 | |
| 34 auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as') | |
| 35 | |
| 36 with open(myBigBedFilePath, 'w') as bigBedFile: | |
| 37 subtools.bedToBigBed(sortedBedFile.name, | |
| 38 self.chromSizesFile.name, | |
| 39 bigBedFile.name, | |
| 40 typeOption='bed4+12', | |
| 41 autoSql=auto_sql_option) | |
| 42 | |
| 43 # Create the Track Object | |
| 44 self.createTrack(file_path=trackName, | |
| 45 track_name=trackName, | |
| 46 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', | |
| 47 priority=self.priority, | |
| 48 track_file=myBigBedFilePath, | |
| 49 track_color=self.track_color, | |
| 50 group_name=self.group_name) | |
| 51 | |
| 52 # dataURL = "tracks/%s" % trackName | |
| 53 # | |
| 54 # trackDb = TrackDb( | |
| 55 # trackName=trackName, | |
| 56 # longLabel=self.name_bed_simple_repeats, | |
| 57 # shortLabel=self.getShortName( self.name_bed_simple_repeats ), | |
| 58 # trackDataURL=dataURL, | |
| 59 # trackType='bigBed 4 +', | |
| 60 # visibility='dense', | |
| 61 # priority=self.priority, | |
| 62 # ) | |
| 63 # | |
| 64 # self.track = Track( | |
| 65 # trackFile=myBigBedFilePath, | |
| 66 # trackDb=trackDb, | |
| 67 # ) | |
| 68 | |
| 69 print("- Bed simple repeats %s created" % self.name_bed_simple_repeats) | |
| 70 #print("- %s created in %s" % (trackName, myBigBedFilePath)) |