Mercurial > repos > rmarenco > hubarchivecreator

annotate BedSimpleRepeats.py @ 12:747475757cb0 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 85389def8ed35b3dc08701963dcae4afd1b5b50a
author rmarenco
date Wed, 27 Jul 2016 10:43:58 -0400
parents d05236b15f81
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 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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13 def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):
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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 self.createTrack(file_path=trackName,
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38 track_name=trackName,
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39 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
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40 priority=self.priority,
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41 track_file=myBigBedFilePath)
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43 # dataURL = "tracks/%s" % trackName
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44 #
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45 # trackDb = TrackDb(
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46 # trackName=trackName,
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47 # longLabel=self.name_bed_simple_repeats,
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48 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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49 # trackDataURL=dataURL,
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50 # trackType='bigBed 4 +',
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51 # visibility='dense',
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52 # priority=self.priority,
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53 # )
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54 #
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55 # self.track = Track(
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56 # trackFile=myBigBedFilePath,
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57 # trackDb=trackDb,
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58 # )
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60 print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
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61 #print("- %s created in %s" % (trackName, myBigBedFilePath))