Mercurial > repos > rmarenco > hubarchivecreator

annotate BedBlastAlignments.py @ 27:cdd33c5c8ac1 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 05fc99e5a081e3f2a0f152ad952ba60c50661229
author yating-l
date Mon, 10 Jul 2017 12:28:50 -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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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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24 self.database = data_bed_blast_alignments["database"]
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25 if data_bed_blast_alignments["long_label"]:
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26 self.long_label = data_bed_blast_alignments["long_label"]
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27 else:
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28 self.long_label = self.name_bed_blast_alignments
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29 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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31 # Sort processing
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32 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
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34 # bedToBigBed processing
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35 # TODO: Change the name of the bb, to tool + genome + .bb
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36 trackName = "".join( ( self.name_bed_blast_alignments, '.bb' ) )
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38 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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40 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
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42 with open(myBigBedFilePath, 'w') as bigBedFile:
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43 subtools.bedToBigBed(self.input_bed_blast_alignments_false_path,
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44 self.chromSizesFile.name,
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45 bigBedFile.name,
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46 typeOption='bed12+12',
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47 tab='True',
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48 autoSql=auto_sql_option,
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49 extraIndex='name')
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51 self.createTrack(file_path=trackName,
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52 track_name=trackName,
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53 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
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54 priority=self.priority,
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55 track_file=myBigBedFilePath,
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56 track_color=self.track_color,
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57 group_name=self.group_name,
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58 database=self.database
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59 )
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62 # dataURL = "tracks/%s" % trackName
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63 #
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64 # trackDb = TrackDb(
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65 # trackName=trackName,
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66 # longLabel=self.name_bed_simple_repeats,
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67 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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68 # trackDataURL=dataURL,
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69 # trackType='bigBed 4 +',
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70 # visibility='dense',
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71 # priority=self.priority,
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72 # )
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73 #
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74 # self.track = Track(
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75 # trackFile=myBigBedFilePath,
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76 # trackDb=trackDb,
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77 # )
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79 print("- Bed Blast alignments %s created" % self.name_bed_blast_alignments)
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80 #print("- %s created in %s" % (trackName, myBigBedFilePath))