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annotate BigWig.py @ 0:3e0c61b52a06 draft

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planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
author yating-l
date Mon, 31 Oct 2016 16:36:25 -0400
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children c66803bff0cc
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3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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1 #!/usr/bin/python
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3 import os
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4 import shutil
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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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12 class BigWig( Datatype ):
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13 def __init__(self, input_bigwig_path, data_bigwig):
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14 super(BigWig, self).__init__()
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16 self.track = None
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18 self.input_bigwig_path = input_bigwig_path
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19 self.name_bigwig = data_bigwig["name"]
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20 self.priority = data_bigwig["order_index"]
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21 self.track_color = data_bigwig["track_color"]
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22 # TODO: Think about how to avoid repetition of the group_name everywhere
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23 self.group_name = data_bigwig["group_name"]
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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 self.createTrack(file_path=trackName,
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34 track_name=trackName,
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35 long_label=self.name_bigwig,
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36 track_type='bigWig', visibility='full',
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37 priority=self.priority,
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38 track_file=myBigWigFilePath,
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39 track_color=self.track_color,
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40 group_name=self.group_name)
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41
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42 # dataURL = "tracks/%s" % trackName
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43 #
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44 # # Return the BigBed track
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45 #
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46 # trackDb = TrackDb(
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47 # trackName=trackName,
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48 # longLabel=self.name_bigwig,
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49 # shortLabel=self.getShortName( self.name_bigwig ),
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50 # trackDataURL=dataURL,
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51 # trackType='bigWig',
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52 # visibility='full',
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53 # priority=self.priority,
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54 # )
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55 #
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56 # self.track = Track(
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57 # trackFile=myBigWigFilePath,
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58 # trackDb=trackDb,
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59 # )
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60
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61 print("- BigWig %s created" % self.name_bigwig)
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62 #print("- %s created in %s" % (trackName, myBigWigFilePath))