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annotate BedSimpleRepeats.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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rmarenco
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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 from Datatype import Datatype
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7 from Track import Track
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8 from TrackDb import TrackDb
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9 from util import subtools
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12 class BedSimpleRepeats( Datatype ):
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rmarenco
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13 def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):
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rmarenco
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15 super(BedSimpleRepeats, self).__init__()
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17 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
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18 self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
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19 self.priority = data_bed_simple_repeats["order_index"]
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21 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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23 # Sort processing
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24 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
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26 # bedToBigBed processing
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27 # TODO: Change the name of the bb, to tool + genome + .bb
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28 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
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29 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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30 auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
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31 with open(myBigBedFilePath, 'w') as bigBedFile:
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32 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
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33 typeOption='-type=bed4+12',
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34 autoSql=auto_sql_option)
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36 # Create the Track Object
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37 dataURL = "tracks/%s" % trackName
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39 trackDb = TrackDb(
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40 trackName=trackName,
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41 longLabel=self.name_bed_simple_repeats,
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42 shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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43 trackDataURL=dataURL,
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44 trackType='bigBed 4 +',
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45 visibility='dense',
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46 priority=self.priority,
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47 )
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49 self.track = Track(
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50 trackFile=myBigBedFilePath,
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51 trackDb=trackDb,
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52 )
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54 print("- %s created in %s" % (trackName, myBigBedFilePath))