Mercurial > repos > rmarenco > hubarchivecreator

annotate BedSpliceJunctions.py @ 28:6aa28a85cc38 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060
author yating-l
date Mon, 10 Jul 2017 17:08:38 -0400
parents df42241d3731
children
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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 BedSpliceJunctions( Datatype ):
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13 def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions):
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15 super(BedSpliceJunctions, self).__init__()
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17 self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path
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18 self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
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19 self.priority = data_bed_splice_junctions["order_index"]
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20 self.track_color = data_bed_splice_junctions["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_splice_junctions["group_name"]
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23 self.database = data_bed_splice_junctions["database"]
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24 if data_bed_splice_junctions["long_label"]:
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25 self.long_label = data_bed_splice_junctions["long_label"]
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26 else:
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27 self.long_label = self.name_bed_splice_junctions
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28 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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30 # Sort processing
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31 subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
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33 # bedToBigBed processing
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34 # TODO: Change the name of the bb, to tool + genome + .bb
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35 trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) )
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36 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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38 auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as')
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40 with open(myBigBedFilePath, 'w') as bigBedFile:
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41 subtools.bedToBigBed(sortedBedFile.name,
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42 self.chromSizesFile.name,
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43 bigBedFile.name,
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44 typeOption='bed12+1',
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45 autoSql=auto_sql_option,
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46 extraIndex='name'
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47 )
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49 # Create the Track Object
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50 self.createTrack(file_path=trackName,
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51 track_name=trackName,
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52 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
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53 priority=self.priority,
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54 track_file=myBigBedFilePath,
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55 track_color=self.track_color,
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56 group_name=self.group_name,
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57 database=self.database)
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58
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59 # dataURL = "tracks/%s" % trackName
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60 #
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61 # trackDb = TrackDb(
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62 # trackName=trackName,
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63 # longLabel=self.name_bed_simple_repeats,
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64 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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65 # trackDataURL=dataURL,
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66 # trackType='bigBed 4 +',
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67 # visibility='dense',
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68 # priority=self.priority,
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69 # )
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70 #
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71 # self.track = Track(
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72 # trackFile=myBigBedFilePath,
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73 # trackDb=trackDb,
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74 # )
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75
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76 print("- Bed splice junctions %s created" % self.name_bed_splice_junctions)
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77 #print("- %s created in %s" % (trackName, myBigBedFilePath))