Mercurial > repos > yating-l > hubarchivecreator

comparison hubArchiveCreator.py @ 5:7b0d359de7ee 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 17:26:51 -0500
parents 44577d6784b7
children 2cc7685a7182
comparison
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4:9018229c0969 5:7b0d359de7ee
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
22 from Bed import Bed 21 from Bed import Bed
23 from BigWig import BigWig 22 from BigWig import BigWig
24 from util.Fasta import Fasta 23 from util.Fasta import Fasta
25 from util.Filters import TraceBackFormatter 24 from util.Filters import TraceBackFormatter
26 from Gff3 import Gff3 25 from Gff3 import Gff3
45 parser.add_argument('--gtf', action='append', help='GTF format') 44 parser.add_argument('--gtf', action='append', help='GTF format')
46 45
47 # Bed4+12 (TrfBig) 46 # Bed4+12 (TrfBig)
48 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as') 47 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
49 48
50 # Bed12+1 (regtools)
51 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
52
53 # Generic Bed (Blastx transformed to bed) 49 # Generic Bed (Blastx transformed to bed)
54 parser.add_argument('--bed', action='append', help='Bed generic format') 50 parser.add_argument('--bed', action='append', help='Bed generic format')
55 51
56 # BigWig Management 52 # BigWig Management
57 parser.add_argument('--bigwig', action='append', help='BigWig format') 53 parser.add_argument('--bigwig', action='append', help='BigWig format')
115 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}] 111 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
116 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH} 112 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
117 array_inputs_bam = args.bam 113 array_inputs_bam = args.bam
118 array_inputs_bed_generic = args.bed 114 array_inputs_bed_generic = args.bed
119 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 115 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
120 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
121 array_inputs_bigwig = args.bigwig 116 array_inputs_bigwig = args.bigwig
122 array_inputs_gff3 = args.gff3 117 array_inputs_gff3 = args.gff3
123 array_inputs_gtf = args.gtf 118 array_inputs_gtf = args.gtf
124 array_inputs_psl = args.psl 119 array_inputs_psl = args.psl
125 120
142 for (inputs, datatype_class) in [ 137 for (inputs, datatype_class) in [
143 (array_inputs_bam, Bam), 138 (array_inputs_bam, Bam),
144 (array_inputs_bed_generic, Bed), 139 (array_inputs_bed_generic, Bed),
145 (array_inputs_bigwig, BigWig), 140 (array_inputs_bigwig, BigWig),
146 (array_inputs_bed_simple_repeats, BedSimpleRepeats), 141 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
147 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
148 (array_inputs_gff3, Gff3), 142 (array_inputs_gff3, Gff3),
149 (array_inputs_gtf, Gtf), 143 (array_inputs_gtf, Gtf),
150 (array_inputs_psl, Psl)]: 144 (array_inputs_psl, Psl)]:
151 if inputs: 145 if inputs:
152 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) 146 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))