Mercurial > repos > rmarenco > hubarchivecreator
comparison Gff3.py @ 10:acc233161f50 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author | rmarenco |
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date | Thu, 21 Jul 2016 05:58:51 -0400 |
parents | fb5e60d4d18a |
children | d05236b15f81 |
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9:4f9847539a28 | 10:acc233161f50 |
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9 from TrackDb import TrackDb | 9 from TrackDb import TrackDb |
10 from util import subtools | 10 from util import subtools |
11 | 11 |
12 | 12 |
13 class Gff3( Datatype ): | 13 class Gff3( Datatype ): |
14 def __init__( self, input_Gff3_false_path, data_gff3, | 14 def __init__(self, input_Gff3_false_path, data_gff3): |
15 input_fasta_false_path, extra_files_path, tool_directory ): | 15 super( Gff3, self ).__init__() |
16 super( Gff3, self ).__init__( | |
17 input_fasta_false_path, extra_files_path, tool_directory | |
18 ) | |
19 | 16 |
20 self.track = None | 17 self.track = None |
21 | 18 |
22 self.input_Gff3_false_path = input_Gff3_false_path | 19 self.input_Gff3_false_path = input_Gff3_false_path |
23 self.name_gff3 = data_gff3["name"] | 20 self.name_gff3 = data_gff3["name"] |
27 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") | 24 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") |
28 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed") | 25 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed") |
29 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | 26 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") |
30 | 27 |
31 # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py) | 28 # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py) |
32 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) | |
33 chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") | |
34 | 29 |
35 # gff3ToGenePred processing | 30 # gff3ToGenePred processing |
36 subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name) | 31 subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name) |
37 | 32 |
38 # TODO: From there, refactor because common use with Gtf.py | 33 # TODO: From there, refactor because common use with Gtf.py |
40 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name) | 35 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name) |
41 | 36 |
42 # Sort processing | 37 # Sort processing |
43 subtools.sort(unsortedBedFile.name, sortedBedFile.name) | 38 subtools.sort(unsortedBedFile.name, sortedBedFile.name) |
44 | 39 |
45 # Generate the twoBitInfo | |
46 subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name) | |
47 | |
48 # Then we get the output to generate the chromSizes | |
49 # TODO: Check if no errors | 40 # TODO: Check if no errors |
50 subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name) | |
51 | 41 |
52 # bedToBigBed processing | 42 # bedToBigBed processing |
53 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb | 43 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb |
54 trackName = "".join( (self.name_gff3, ".bb" ) ) | 44 trackName = "".join( (self.name_gff3, ".bb" ) ) |
55 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | 45 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) |
56 with open(myBigBedFilePath, 'w') as bigBedFile: | 46 with open(myBigBedFilePath, 'w') as bigBedFile: |
57 subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name) | 47 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) |
58 | 48 |
59 # Create the Track Object | 49 # Create the Track Object |
60 dataURL = "tracks/%s" % trackName | 50 dataURL = "tracks/%s" % trackName |
61 | 51 |
62 trackDb = TrackDb( | 52 trackDb = TrackDb( |