Mercurial > repos > yating-l > hubarchivecreator

comparison hubArchiveCreator.py @ 9:d5781fe7b782 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
author yating-l
date Wed, 28 Dec 2016 17:33:08 -0500
parents be8fd2f24c60
children
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8:be8fd2f24c60 9:d5781fe7b782
16 import sys 16 import sys
17 17
18 # Internal dependencies 18 # Internal dependencies
19 from Bam import Bam 19 from Bam import Bam
20 from BedSimpleRepeats import BedSimpleRepeats 20 from BedSimpleRepeats import BedSimpleRepeats
21 from BedSpliceJunctions import BedSpliceJunctions
21 from Bed import Bed 22 from Bed import Bed
22 from BigWig import BigWig 23 from BigWig import BigWig
23 from util.Fasta import Fasta 24 from util.Fasta import Fasta
24 from util.Filters import TraceBackFormatter 25 from util.Filters import TraceBackFormatter
25 from Gff3 import Gff3 26 from Gff3 import Gff3
26 from Gtf import Gtf 27 from Gtf import Gtf
27 from Psl import Psl 28 from Psl import Psl
28 from TrackHub import TrackHub 29 from TrackHub import TrackHub
30 from bigPsl import bigPsl
29 31
30 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort 32 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
31 33
32 34
33 def main(argv): 35 def main(argv):
44 parser.add_argument('--gtf', action='append', help='GTF format') 46 parser.add_argument('--gtf', action='append', help='GTF format')
45 47
46 # Bed4+12 (TrfBig) 48 # Bed4+12 (TrfBig)
47 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as') 49 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
48 50
51 # Bed12+1 (regtools)
52 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
53
49 # Generic Bed (Blastx transformed to bed) 54 # Generic Bed (Blastx transformed to bed)
50 parser.add_argument('--bed', action='append', help='Bed generic format') 55 parser.add_argument('--bed', action='append', help='Bed generic format')
56
57 # Bed12+12 (tblastn)
58 parser.add_argument('--bigpsl', action='append', help='bigPsl format')
51 59
52 # BigWig Management 60 # BigWig Management
53 parser.add_argument('--bigwig', action='append', help='BigWig format') 61 parser.add_argument('--bigwig', action='append', help='BigWig format')
54 62
55 # Bam Management 63 # Bam Management
111 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}] 119 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
112 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH} 120 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
113 array_inputs_bam = args.bam 121 array_inputs_bam = args.bam
114 array_inputs_bed_generic = args.bed 122 array_inputs_bed_generic = args.bed
115 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 123 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
124 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
116 array_inputs_bigwig = args.bigwig 125 array_inputs_bigwig = args.bigwig
117 array_inputs_gff3 = args.gff3 126 array_inputs_gff3 = args.gff3
118 array_inputs_gtf = args.gtf 127 array_inputs_gtf = args.gtf
119 array_inputs_psl = args.psl 128 array_inputs_psl = args.psl
129 array_inputs_bigpsl = args.bigpsl
120 130
121 outputFile = args.output 131 outputFile = args.output
122 132
123 json_inputs_data = args.data_json 133 json_inputs_data = args.data_json
124 134
137 for (inputs, datatype_class) in [ 147 for (inputs, datatype_class) in [
138 (array_inputs_bam, Bam), 148 (array_inputs_bam, Bam),
139 (array_inputs_bed_generic, Bed), 149 (array_inputs_bed_generic, Bed),
140 (array_inputs_bigwig, BigWig), 150 (array_inputs_bigwig, BigWig),
141 (array_inputs_bed_simple_repeats, BedSimpleRepeats), 151 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
152 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
142 (array_inputs_gff3, Gff3), 153 (array_inputs_gff3, Gff3),
143 (array_inputs_gtf, Gtf), 154 (array_inputs_gtf, Gtf),
144 (array_inputs_psl, Psl)]: 155 (array_inputs_psl, Psl),
156 (array_inputs_bigpsl, bigPsl)]:
145 if inputs: 157 if inputs:
146 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) 158 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
147 159
148 # Create Ordered Dictionary to add the tracks in the tool form order 160 # Create Ordered Dictionary to add the tracks in the tool form order
149 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) 161 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)