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annotate Bed.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents fb5e60d4d18a
children d05236b15f81
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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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rmarenco
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14 def __init__( self, inputBedGeneric, data_bed_generic):
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rmarenco
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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 dataURL = "tracks/%s" % trackName
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41 trackDb = TrackDb(
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42 trackName=trackName,
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43 longLabel=self.name_bed_generic,
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44 shortLabel=self.getShortName(self.name_bed_generic),
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45 trackDataURL=dataURL,
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46 trackType='bigBed',
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47 visibility='dense',
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48 thickDrawItem='on',
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49 priority=self.priority,
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50 )
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52 # Return the BigBed track
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53 self.track = Track(
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54 trackFile=myBigBedFilePath,
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55 trackDb=trackDb,
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56 )
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58 print("- %s created in %s" % (trackName, myBigBedFilePath))