Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.py @ 21:884ee2a71680 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 15:05:33 -0400
parents 40469b265ddb
children fcc1021bd496
comparison
equal deleted inserted replaced
20:40469b265ddb 21:884ee2a71680
26 from Gff3 import Gff3 26 from Gff3 import Gff3
27 from Gtf import Gtf 27 from Gtf import Gtf
28 from Psl import Psl 28 from Psl import Psl
29 from TrackHub import TrackHub 29 from TrackHub import TrackHub
30 from bigPsl import bigPsl 30 from bigPsl import bigPsl
31 from BedBlastAlignments import BedBlastAlignments
31 32
32 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort 33 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
33 34
34 35
35 def main(argv): 36 def main(argv):
52 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as') 53 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
53 54
54 # Generic Bed (Blastx transformed to bed) 55 # Generic Bed (Blastx transformed to bed)
55 parser.add_argument('--bed', action='append', help='Bed generic format') 56 parser.add_argument('--bed', action='append', help='Bed generic format')
56 57
57 # Bed12+12 (tblastn) 58 # BigPsl (blat alignment)
58 parser.add_argument('--bigpsl', action='append', help='bigPsl format') 59 parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
60
61 # Bed12+12 (tblastn alignment)
62 parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')
59 63
60 # BigWig Management 64 # BigWig Management
61 parser.add_argument('--bigwig', action='append', help='BigWig format') 65 parser.add_argument('--bigwig', action='append', help='BigWig format')
62 66
63 # Bam Management 67 # Bam Management
125 array_inputs_bigwig = args.bigwig 129 array_inputs_bigwig = args.bigwig
126 array_inputs_gff3 = args.gff3 130 array_inputs_gff3 = args.gff3
127 array_inputs_gtf = args.gtf 131 array_inputs_gtf = args.gtf
128 array_inputs_psl = args.psl 132 array_inputs_psl = args.psl
129 array_inputs_bigpsl = args.bigpsl 133 array_inputs_bigpsl = args.bigpsl
134 array_inputs_bed_blast_alignments = args.bedBlastAlignments
130 135
131 outputFile = args.output 136 outputFile = args.output
132 137
133 json_inputs_data = args.data_json 138 json_inputs_data = args.data_json
134 139
151 (array_inputs_bed_simple_repeats, BedSimpleRepeats), 156 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
152 (array_inputs_bed_splice_junctions, BedSpliceJunctions), 157 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
153 (array_inputs_gff3, Gff3), 158 (array_inputs_gff3, Gff3),
154 (array_inputs_gtf, Gtf), 159 (array_inputs_gtf, Gtf),
155 (array_inputs_psl, Psl), 160 (array_inputs_psl, Psl),
156 (array_inputs_bigpsl, bigPsl)]: 161 (array_inputs_bigpsl, bigPsl),
162 (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
157 if inputs: 163 if inputs:
158 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) 164 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
159 165
160 # Create Ordered Dictionary to add the tracks in the tool form order 166 # Create Ordered Dictionary to add the tracks in the tool form order
161 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) 167 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)