Mercurial > repos > yating-l > hubarchivecreator

annotate Bed.py @ 0:3e0c61b52a06 draft

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planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
author yating-l
date Mon, 31 Oct 2016 16:36:25 -0400
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children 4ced8f116509
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3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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1 #!/usr/bin/python
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2
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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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12
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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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30 modified = self._checkAndFixBed()
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31 # Sort processing
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32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
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37 # bedToBigBed processing
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38 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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39 trackName = "".join( ( self.name_bed_generic, ".bb") )
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40
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41 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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42 with open(myBigBedFilePath, 'w') as self.bigBedFile:
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43 subtools.bedToBigBed(self.sortedBedFile.name,
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44 self.chromSizesFile.name,
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45 self.bigBedFile.name,
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46 typeOption='bed12+1',
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47 tab=True)
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48
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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.name_bed_generic, track_type='bigBed', 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 )
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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_generic,
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64 # shortLabel=self.getShortName(self.name_bed_generic),
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65 # trackDataURL=dataURL,
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66 # trackType='bigBed',
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67 # visibility='dense',
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68 # thickDrawItem='on',
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69 # priority=self.priority,
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70 # )
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71 #
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72 # # Return the BigBed track
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73 # self.track = Track(
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74 # trackFile=myBigBedFilePath,
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75 # trackDb=trackDb,
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76 # )
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77
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78 print("- Bed %s created" % self.name_bed_generic)
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79 if (len(modified) != 0):
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80 print("The lines that were removed: " + str(len(modified)))
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81 #print("- %s created in %s" % (trackName, myBigBedFilePath))
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82
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83 # TODO: bed verifier, check if there are invalid strands: "."
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84 def _checkAndFixBed(self):
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85 """
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86 Call _checkAndFixBed, check the integrity of bed file,
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87 if the strand is not "+" or "-" truncate that line and report to users
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88 create column and move the score column to
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89 """
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90 # Store the lines that have been removed
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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91 removedLines = []
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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92 # Remove the lines with invalid strand
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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93 temp_bed = tempfile.NamedTemporaryFile(bufsize=0, suffix=".bed", delete=False)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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94 with open(temp_bed.name, 'w') as tmp:
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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95 with open(self.inputBedGeneric, 'r') as f:
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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96 lines = f.readlines()
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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97 for line in lines:
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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98 fields = line.split()
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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99 strand = fields[5]
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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100 score = fields[4]
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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101 fields[4] = '1000'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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102 fields.append(score)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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103 if (strand == '+' or strand == '-'):
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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104 tmp.write('\t'.join(map(str, fields)))
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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105 tmp.write("\n")
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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106 else:
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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107 removedLines.append(line)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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108 self.inputBedGeneric = temp_bed.name
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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109
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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110 return removedLines