Mercurial > repos > rmarenco > hubarchivecreator

annotate BedBlastAlignments.py @ 22:7ddf651457df draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 17:03:51 -0400
parents 884ee2a71680
children 2677f1899aa8
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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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5 import string
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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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10 from util import subtools
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13 class BedBlastAlignments( Datatype ):
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14 def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments):
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16 super(BedBlastAlignments, self).__init__()
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18 self.input_bed_blast_alignments_false_path = input_bed_blast_alignments_false_path
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19 self.name_bed_blast_alignments = data_bed_blast_alignments["name"]
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20 self.priority = data_bed_blast_alignments["order_index"]
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21 self.track_color = data_bed_blast_alignments["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_bed_blast_alignments["group_name"]
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25 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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27 # Sort processing
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28 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
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30 # bedToBigBed processing
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31 # TODO: Change the name of the bb, to tool + genome + .bb
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32 trackName = "".join( ( self.name_bed_blast_alignments, '.bb' ) )
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34 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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36 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
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38 with open(myBigBedFilePath, 'w') as bigBedFile:
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39 subtools.bedToBigBed(self.input_bed_blast_alignments_false_path,
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40 self.chromSizesFile.name,
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41 bigBedFile.name,
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42 typeOption='bed12+12',
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43 tab='True',
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44 autoSql=auto_sql_option)
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46 self.createTrack(file_path=trackName,
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47 track_name=trackName,
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48 long_label=self.name_bed_blast_alignments, track_type='bigBed 12 +', visibility='dense',
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49 priority=self.priority,
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50 track_file=myBigBedFilePath,
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51 track_color=self.track_color,
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52 group_name=self.group_name)
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55 # dataURL = "tracks/%s" % trackName
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56 #
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57 # trackDb = TrackDb(
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58 # trackName=trackName,
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59 # longLabel=self.name_bed_simple_repeats,
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60 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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61 # trackDataURL=dataURL,
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62 # trackType='bigBed 4 +',
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63 # visibility='dense',
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64 # priority=self.priority,
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65 # )
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66 #
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67 # self.track = Track(
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68 # trackFile=myBigBedFilePath,
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69 # trackDb=trackDb,
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70 # )
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72 print("- Bed Blast alignments %s created" % self.name_bed_blast_alignments)
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73 #print("- %s created in %s" % (trackName, myBigBedFilePath))