Mercurial > repos > yating-l > hubarchivecreator

annotate BedSimpleRepeats.py @ 62:4c4e8941feda draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060-dirty
author yating-l
date Mon, 10 Jul 2017 17:06:11 -0400
parents a0fc8379223c
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 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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23 self.database = data_bed_simple_repeats["database"]
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24 if data_bed_simple_repeats["long_label"]:
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25 self.long_label = data_bed_simple_repeats["long_label"]
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26 else:
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27 self.long_label = self.name_bed_simple_repeats
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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_bed_simple_repeats_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_simple_repeats, '.bb' ) )
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37 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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39 auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
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41 with open(myBigBedFilePath, 'w') as bigBedFile:
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42 subtools.bedToBigBed(sortedBedFile.name,
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43 self.chromSizesFile.name,
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44 bigBedFile.name,
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45 typeOption='bed4+12',
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46 autoSql=auto_sql_option,
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47 extraIndex='name'
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48 )
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49
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50 # Create the Track Object
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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 4 +', 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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60 # dataURL = "tracks/%s" % trackName
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61 #
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62 # trackDb = TrackDb(
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63 # trackName=trackName,
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64 # longLabel=self.name_bed_simple_repeats,
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65 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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66 # trackDataURL=dataURL,
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67 # trackType='bigBed 4 +',
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68 # visibility='dense',
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69 # priority=self.priority,
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70 # )
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71 #
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72 # self.track = Track(
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73 # trackFile=myBigBedFilePath,
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74 # trackDb=trackDb,
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75 # )
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76
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77 print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
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78 #print("- %s created in %s" % (trackName, myBigBedFilePath))