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annotate Bed.py @ 11:d05236b15f81 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author rmarenco
date Wed, 27 Jul 2016 10:10:49 -0400
parents acc233161f50
children 25809f699cb3
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1 #!/usr/bin/python
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3 import os
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4 import tempfile
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6 # Internal dependencies
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7 from Datatype import Datatype
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8 from Track import Track
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9 from TrackDb import TrackDb
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10 from util import subtools
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13 class Bed( Datatype ):
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14 def __init__( self, inputBedGeneric, data_bed_generic):
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15 super(Bed, self).__init__()
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17 self.track = None
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19 self.inputBedGeneric = inputBedGeneric
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21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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23 self.data_bed_generic = data_bed_generic
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24 self.name_bed_generic = self.data_bed_generic["name"]
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25 self.priority = self.data_bed_generic["order_index"]
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27 # Sort processing
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28 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
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30 # bedToBigBed processing
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31 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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32 trackName = "".join( ( self.name_bed_generic, ".bb") )
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34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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35 with open(myBigBedFilePath, 'w') as self.bigBedFile:
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36 subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
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38 # Create the Track Object
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39 self.createTrack(file_path=trackName,
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40 track_name=trackName,
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41 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
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42 priority=self.priority,
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43 track_file=myBigBedFilePath)
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45 # dataURL = "tracks/%s" % trackName
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46 #
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47 # trackDb = TrackDb(
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48 # trackName=trackName,
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49 # longLabel=self.name_bed_generic,
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50 # shortLabel=self.getShortName(self.name_bed_generic),
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51 # trackDataURL=dataURL,
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52 # trackType='bigBed',
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53 # visibility='dense',
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54 # thickDrawItem='on',
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55 # priority=self.priority,
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56 # )
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57 #
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58 # # Return the BigBed track
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59 # self.track = Track(
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60 # trackFile=myBigBedFilePath,
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61 # trackDb=trackDb,
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62 # )
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63
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64 print("- Bed %s created" % self.name_bed_generic)
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65 #print("- %s created in %s" % (trackName, myBigBedFilePath))