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annotate BedSimpleRepeats.py @ 0:abcfd662b679 draft default tip

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author yating-l
date Thu, 22 Dec 2016 17:53:00 -0500
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abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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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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20 self.track_color = data_bed_simple_repeats["track_color"]
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21 # TODO: Think about how to avoid repetition of the group_name everywhere
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22 self.group_name = data_bed_simple_repeats["group_name"]
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24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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26 # Sort processing
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27 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
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29 # bedToBigBed processing
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30 # TODO: Change the name of the bb, to tool + genome + .bb
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31 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
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32 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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34 auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
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36 with open(myBigBedFilePath, 'w') as bigBedFile:
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37 subtools.bedToBigBed(sortedBedFile.name,
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38 self.chromSizesFile.name,
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39 bigBedFile.name,
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40 typeOption='bed4+12',
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41 autoSql=auto_sql_option)
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42
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43 # Create the Track Object
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44 self.createTrack(file_path=trackName,
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45 track_name=trackName,
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46 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
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47 priority=self.priority,
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48 track_file=myBigBedFilePath,
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49 track_color=self.track_color,
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50 group_name=self.group_name)
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51
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52 # dataURL = "tracks/%s" % trackName
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53 #
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54 # trackDb = TrackDb(
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55 # trackName=trackName,
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56 # longLabel=self.name_bed_simple_repeats,
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57 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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58 # trackDataURL=dataURL,
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59 # trackType='bigBed 4 +',
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60 # visibility='dense',
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61 # priority=self.priority,
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62 # )
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63 #
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64 # self.track = Track(
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65 # trackFile=myBigBedFilePath,
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66 # trackDb=trackDb,
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67 # )
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68
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69 print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
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70 #print("- %s created in %s" % (trackName, myBigBedFilePath))