Mercurial > repos > rmarenco > hubarchivecreator
comparison BedSpliceJunctions.py @ 20:40469b265ddb draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
| author | yating-l |
|---|---|
| date | Fri, 20 Jan 2017 17:12:03 -0500 |
| parents | |
| children | 2677f1899aa8 |
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| 19:0152500d9acd | 20:40469b265ddb |
|---|---|
| 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 BedSpliceJunctions( Datatype ): | |
| 13 def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions): | |
| 14 | |
| 15 super(BedSpliceJunctions, self).__init__() | |
| 16 | |
| 17 self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path | |
| 18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"] | |
| 19 self.priority = data_bed_splice_junctions["order_index"] | |
| 20 self.track_color = data_bed_splice_junctions["track_color"] | |
| 21 # TODO: Think about how to avoid repetition of the group_name everywhere | |
| 22 self.group_name = data_bed_splice_junctions["group_name"] | |
| 23 | |
| 24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | |
| 25 | |
| 26 # Sort processing | |
| 27 subtools.sort(self.input_bed_splice_junctions_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_splice_junctions, '.bb' ) ) | |
| 32 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 33 | |
| 34 auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as') | |
| 35 | |
| 36 with open(myBigBedFilePath, 'w') as bigBedFile: | |
| 37 subtools.bedToBigBed(sortedBedFile.name, | |
| 38 self.chromSizesFile.name, | |
| 39 bigBedFile.name, | |
| 40 typeOption='bed12+1', | |
| 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_splice_junctions, track_type='bigBed 12 +', 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 splice junctions %s created" % self.name_bed_splice_junctions) | |
| 70 #print("- %s created in %s" % (trackName, myBigBedFilePath)) |