Mercurial > repos > yating-l > hubarchivecreator

comparison hubArchiveCreator.py @ 3:44577d6784b7 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty
author yating-l
date Wed, 21 Dec 2016 11:18:27 -0500
parents 4ced8f116509
children 7b0d359de7ee
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2:4ced8f116509 3:44577d6784b7
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
44 parser.add_argument('--gtf', action='append', help='GTF format') 45 parser.add_argument('--gtf', action='append', help='GTF format')
45 46
46 # Bed4+12 (TrfBig) 47 # Bed4+12 (TrfBig)
47 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as') 48 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
48 49
50 # Bed12+1 (regtools)
51 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
52
49 # Generic Bed (Blastx transformed to bed) 53 # Generic Bed (Blastx transformed to bed)
50 parser.add_argument('--bed', action='append', help='Bed generic format') 54 parser.add_argument('--bed', action='append', help='Bed generic format')
51 55
52 # BigWig Management 56 # BigWig Management
53 parser.add_argument('--bigwig', action='append', help='BigWig format') 57 parser.add_argument('--bigwig', action='append', help='BigWig format')
111 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}] 115 # 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} 116 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
113 array_inputs_bam = args.bam 117 array_inputs_bam = args.bam
114 array_inputs_bed_generic = args.bed 118 array_inputs_bed_generic = args.bed
115 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 119 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
120 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
116 array_inputs_bigwig = args.bigwig 121 array_inputs_bigwig = args.bigwig
117 array_inputs_gff3 = args.gff3 122 array_inputs_gff3 = args.gff3
118 array_inputs_gtf = args.gtf 123 array_inputs_gtf = args.gtf
119 array_inputs_psl = args.psl 124 array_inputs_psl = args.psl
120 125
137 for (inputs, datatype_class) in [ 142 for (inputs, datatype_class) in [
138 (array_inputs_bam, Bam), 143 (array_inputs_bam, Bam),
139 (array_inputs_bed_generic, Bed), 144 (array_inputs_bed_generic, Bed),
140 (array_inputs_bigwig, BigWig), 145 (array_inputs_bigwig, BigWig),
141 (array_inputs_bed_simple_repeats, BedSimpleRepeats), 146 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
147 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
142 (array_inputs_gff3, Gff3), 148 (array_inputs_gff3, Gff3),
143 (array_inputs_gtf, Gtf), 149 (array_inputs_gtf, Gtf),
144 (array_inputs_psl, Psl)]: 150 (array_inputs_psl, Psl)]:
145 if inputs: 151 if inputs:
146 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) 152 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))