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annotate BigWig.py @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children acc233161f50
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fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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1 #!/usr/bin/python
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3 import os
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rmarenco
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4 import shutil
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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6 # Internal dependencies
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7 from Datatype import Datatype
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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8 from Track import Track
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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9 from TrackDb import TrackDb
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12 class BigWig( Datatype ):
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13 def __init__(self, input_bigwig_path, data_bigwig,
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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14 input_fasta_path, extra_files_path, tool_directory):
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15 super(BigWig, self).__init__(
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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16 input_fasta_path, extra_files_path, tool_directory
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17 )
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19 self.track = None
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21 self.input_bigwig_path = input_bigwig_path
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22 self.name_bigwig = data_bigwig["name"]
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23 self.priority = data_bigwig["order_index"]
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25 print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
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27 trackName = "".join( ( self.name_bigwig, ".bigwig" ) )
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29 myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName)
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30 shutil.copy(self.input_bigwig_path, myBigWigFilePath)
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32 # Create the Track Object
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33 dataURL = "tracks/%s" % trackName
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35 # Return the BigBed track
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36 trackDb = TrackDb(
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37 trackName=trackName,
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38 longLabel=self.name_bigwig,
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39 shortLabel=self.getShortName( self.name_bigwig ),
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40 trackDataURL=dataURL,
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41 trackType='bigWig',
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42 visibility='full',
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43 priority=self.priority,
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44 )
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46 self.track = Track(
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47 trackFile=myBigWigFilePath,
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48 trackDb=trackDb,
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49 )
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51 print("- %s created in %s" % (trackName, myBigWigFilePath))