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annotate Bed.py @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 2677f1899aa8
children 6aa28a85cc38
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rmarenco
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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 # Internal dependencies
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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 Bed( Datatype ):
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14 def __init__( self, inputBedGeneric, data_bed_generic):
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15 super(Bed, self).__init__()
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17 self.track = None
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19 self.inputBedGeneric = inputBedGeneric
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21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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23 self.data_bed_generic = data_bed_generic
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24 self.name_bed_generic = self.data_bed_generic["name"]
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25 self.priority = self.data_bed_generic["order_index"]
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26 self.track_color = self.data_bed_generic["track_color"]
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27 # TODO: Think about how to avoid repetition of the group_name everywhere
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28 self.group_name = self.data_bed_generic["group_name"]
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29 self.database = self.data_bed_generic["database"]
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30 if self.data_bed_generic["long_label"]:
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31 self.long_label = self.data_bed_generic["long_label"]
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32 else:
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33 self.long_label = self.name_bed_generic
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35 # Sort processing
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36 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
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38 # bedToBigBed processing
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39 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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40 trackName = "".join( ( self.name_bed_generic, ".bb") )
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42 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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43 with open(myBigBedFilePath, 'w') as self.bigBedFile:
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44 subtools.bedToBigBed(self.sortedBedFile.name,
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45 self.chromSizesFile.name,
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46 self.bigBedFile.name,
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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', 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_generic,
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65 # shortLabel=self.getShortName(self.name_bed_generic),
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66 # trackDataURL=dataURL,
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67 # trackType='bigBed',
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68 # visibility='dense',
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69 # thickDrawItem='on',
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70 # priority=self.priority,
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71 # )
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72 #
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73 # # Return the BigBed track
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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 # )
1
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78
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79 print("- Bed %s created" % self.name_bed_generic)
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80 #print("- %s created in %s" % (trackName, myBigBedFilePath))