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annotate bigPsl.py @ 34:04b942019dce draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
author yating-l
date Thu, 29 Dec 2016 17:57:51 -0500
parents d5781fe7b782
children 364b8db8de17
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d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-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 bigPsl( Datatype ):
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13 def __init__(self, input_bigpsl_false_path, data_bigpsl):
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15 super(bigPsl, self).__init__()
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17 self.input_bigpsl_false_path = input_bigpsl_false_path
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18 self.name_bigpsl = data_bigpsl["name"]
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19 self.priority = data_bigpsl["order_index"]
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20 self.track_color = data_bigpsl["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_bigpsl["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_bigpsl_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_bigpsl, '.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, 'bigPsl.as')
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36 with open(myBigBedFilePath, 'w') as bigBedFile:
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37 subtools.bedToBigBed(self.input_bigpsl_false_path,
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38 self.chromSizesFile.name,
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39 bigBedFile.name,
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40 typeOption='bed12+12',
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41 tab='True',
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42 autoSql=auto_sql_option)
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44 # Create the Track Object
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45 self.createTrack(file_path=trackName,
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46 track_name=trackName,
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47 long_label=self.name_bigpsl, track_type='bigBed 12 +', visibility='dense',
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48 priority=self.priority,
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49 track_file=myBigBedFilePath,
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50 track_color=self.track_color,
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51 group_name=self.group_name)
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52
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53 # dataURL = "tracks/%s" % trackName
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54 #
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55 # trackDb = TrackDb(
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56 # trackName=trackName,
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57 # longLabel=self.name_bed_simple_repeats,
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58 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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59 # trackDataURL=dataURL,
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60 # trackType='bigBed 4 +',
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61 # visibility='dense',
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62 # priority=self.priority,
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63 # )
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64 #
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65 # self.track = Track(
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66 # trackFile=myBigBedFilePath,
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67 # trackDb=trackDb,
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68 # )
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69
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70 print("- bigPsl %s created" % self.name_bigpsl)
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71 #print("- %s created in %s" % (trackName, myBigBedFilePath))