Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children 3233451a3bd6
comparison
equal deleted inserted replaced
12:747475757cb0 13:25809f699cb3
19 self.input_Gff3_false_path = input_Gff3_false_path 19 self.input_Gff3_false_path = input_Gff3_false_path
20 self.name_gff3 = data_gff3["name"] 20 self.name_gff3 = data_gff3["name"]
21 self.priority = data_gff3["order_index"] 21 self.priority = data_gff3["order_index"]
22 22
23 # TODO: See if we need these temporary files as part of the generated files 23 # TODO: See if we need these temporary files as part of the generated files
24 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 24 unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
25 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed") 25 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
26 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 26 sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
27
28 # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)
29 27
30 # gff3ToGenePred processing 28 # gff3ToGenePred processing
31 subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name) 29 subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
32 30
33 # TODO: From there, refactor because common use with Gtf.py 31 # genePredToBigGenePred
34 # genePredToBed processing 32 subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
35 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
36 33
37 # Sort processing 34 # Sort processing
38 subtools.sort(unsortedBedFile.name, sortedBedFile.name) 35 subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
39 36
40 # TODO: Check if no errors 37 # TODO: Check if no errors
41 38
42 # bedToBigBed processing 39 # bedToBigBed processing
43 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
44 trackName = "".join( (self.name_gff3, ".bb" ) ) 40 trackName = "".join( (self.name_gff3, ".bb" ) )
41
42 auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
43
45 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) 44 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
45
46 with open(myBigBedFilePath, 'w') as bigBedFile: 46 with open(myBigBedFilePath, 'w') as bigBedFile:
47 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) 47 subtools.bedToBigBed(sorted_biGenePred_file.name,
48 self.chromSizesFile.name,
49 bigBedFile.name,
50 autoSql=auto_sql_option,
51 typeOption='bed12+8',
52 tab=True)
48 53
49 # Create the Track Object 54 # Create the Track Object
50 self.createTrack(file_path=trackName, 55 self.createTrack(file_path=trackName,
51 track_name=trackName, 56 track_name=trackName,
52 long_label=self.name_gff3, track_type='bigBed 12 +', visibility='dense', priority=self.priority, 57 long_label=self.name_gff3,
58 track_type='bigGenePred', visibility='dense',
59 priority=self.priority,
53 track_file=myBigBedFilePath) 60 track_file=myBigBedFilePath)
54 61
55 # dataURL = "tracks/%s" % trackName
56 #
57 # trackDb = TrackDb(
58 # trackName=trackName,
59 # longLabel=self.name_gff3,
60 # shortLabel=self.getShortName( self.name_gff3 ),
61 # trackDataURL=dataURL,
62 # trackType='bigBed 12 +',
63 # visibility='dense',
64 # priority=self.priority,
65 # )
66 #
67 # self.track = Track(
68 # trackFile=myBigBedFilePath,
69 # trackDb=trackDb,
70 # )
71
72 print("- Gff3 %s created" % self.name_gff3) 62 print("- Gff3 %s created" % self.name_gff3)
73 #print("- %s created in %s" % (trackName, myBigBedFilePath))