Mercurial > repos > yating-l > hubarchivecreator

comparison Bed.py @ 2:4ced8f116509 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
author yating-l
date Tue, 22 Nov 2016 17:13:18 -0500
parents 3e0c61b52a06
children
comparison
equal deleted inserted replaced
1:42337785f87b 2:4ced8f116509
24 self.name_bed_generic = self.data_bed_generic["name"] 24 self.name_bed_generic = self.data_bed_generic["name"]
25 self.priority = self.data_bed_generic["order_index"] 25 self.priority = self.data_bed_generic["order_index"]
26 self.track_color = self.data_bed_generic["track_color"] 26 self.track_color = self.data_bed_generic["track_color"]
27 # TODO: Think about how to avoid repetition of the group_name everywhere 27 # TODO: Think about how to avoid repetition of the group_name everywhere
28 self.group_name = self.data_bed_generic["group_name"] 28 self.group_name = self.data_bed_generic["group_name"]
29 29
30 modified = self._checkAndFixBed() 30
31 # Sort processing 31 # Sort processing
32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) 32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
33
34
35
36 33
37 # bedToBigBed processing 34 # bedToBigBed processing
38 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb 35 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
39 trackName = "".join( ( self.name_bed_generic, ".bb") ) 36 trackName = "".join( ( self.name_bed_generic, ".bb") )
40 37
41 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 38 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
42 with open(myBigBedFilePath, 'w') as self.bigBedFile: 39 with open(myBigBedFilePath, 'w') as self.bigBedFile:
43 subtools.bedToBigBed(self.sortedBedFile.name, 40 subtools.bedToBigBed(self.sortedBedFile.name,
44 self.chromSizesFile.name, 41 self.chromSizesFile.name,
45 self.bigBedFile.name, 42 self.bigBedFile.name)
46 typeOption='bed12+1', 43
47 tab=True)
48
49 # Create the Track Object 44 # Create the Track Object
50 self.createTrack(file_path=trackName, 45 self.createTrack(file_path=trackName,
51 track_name=trackName, 46 track_name=trackName,
52 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', 47 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
53 priority=self.priority, 48 priority=self.priority,
54 track_file=myBigBedFilePath, 49 track_file=myBigBedFilePath,
55 track_color=self.track_color, 50 track_color=self.track_color,
56 group_name=self.group_name, 51 group_name=self.group_name)
57 )
58 52
59 # dataURL = "tracks/%s" % trackName 53 # dataURL = "tracks/%s" % trackName
60 # 54 #
61 # trackDb = TrackDb( 55 # trackDb = TrackDb(
62 # trackName=trackName, 56 # trackName=trackName,
74 # trackFile=myBigBedFilePath, 68 # trackFile=myBigBedFilePath,
75 # trackDb=trackDb, 69 # trackDb=trackDb,
76 # ) 70 # )
77 71
78 print("- Bed %s created" % self.name_bed_generic) 72 print("- Bed %s created" % self.name_bed_generic)
79 if (len(modified) != 0):
80 print("The lines that were removed: " + str(len(modified)))
81 #print("- %s created in %s" % (trackName, myBigBedFilePath)) 73 #print("- %s created in %s" % (trackName, myBigBedFilePath))
82
83 # TODO: bed verifier, check if there are invalid strands: "."
84 def _checkAndFixBed(self):
85 """
86 Call _checkAndFixBed, check the integrity of bed file,
87 if the strand is not "+" or "-" truncate that line and report to users
88 create column and move the score column to
89 """
90 # Store the lines that have been removed
91 removedLines = []
92 # Remove the lines with invalid strand
93 temp_bed = tempfile.NamedTemporaryFile(bufsize=0, suffix=".bed", delete=False)
94 with open(temp_bed.name, 'w') as tmp:
95 with open(self.inputBedGeneric, 'r') as f:
96 lines = f.readlines()
97 for line in lines:
98 fields = line.split()
99 strand = fields[5]
100 score = fields[4]
101 fields[4] = '1000'
102 fields.append(score)
103 if (strand == '+' or strand == '-'):
104 tmp.write('\t'.join(map(str, fields)))
105 tmp.write("\n")
106 else:
107 removedLines.append(line)
108 self.inputBedGeneric = temp_bed.name
109
110 return removedLines