Mercurial > repos > yating-l > jbrowse_hub

comparison jbrowse_hub.py @ 12:e1f188b43750 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 14:31:36 -0400
parents e7c80e9b70ae
children f2285f29a6fa
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11:22efe9f6e8a8 12:e1f188b43750
25 parser.add_argument('-o', '--out', help='output html') 25 parser.add_argument('-o', '--out', help='output html')
26 26
27 # Output folder 27 # Output folder
28 parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder") 28 parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")
29 29
30 # GFF3 30 # GFF3 structure: gene->transcription->CDS
31 parser.add_argument('--gff3', action='append', help='GFF3 format') 31 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS')
32
33 # GFF3 structure: gene->mRNA->CDS
34 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')
32 35
33 # trfBig simple repeats (BED 4+12) 36 # trfBig simple repeats (BED 4+12)
34 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as') 37 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
35 38
36 # regtools (BED 12+1) 39 # regtools (BED 12+1)
71 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks 74 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
72 array_inputs_bam = args.bam 75 array_inputs_bam = args.bam
73 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 76 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
74 array_inputs_bed_splice_junctions = args.bedSpliceJunctions 77 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
75 array_inputs_bigwig = args.bigwig 78 array_inputs_bigwig = args.bigwig
76 array_inputs_gff3 = args.gff3 79 array_inputs_gff3_transcript = args.gff3_transcript
80 array_inputs_gff3_mrna = args.gff3_mrna
77 array_inputs_gtf = args.gtf 81 array_inputs_gtf = args.gtf
78 array_inputs_blastxml = args.blastxml 82 array_inputs_blastxml = args.blastxml
79 if array_inputs_bam: 83 if array_inputs_bam:
80 all_datatype_dictionary['bam'] = array_inputs_bam 84 all_datatype_dictionary['bam'] = array_inputs_bam
81 if array_inputs_bed_simple_repeats: 85 if array_inputs_bed_simple_repeats:
82 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats 86 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
83 if array_inputs_bed_splice_junctions: 87 if array_inputs_bed_splice_junctions:
84 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions 88 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
85 if array_inputs_bigwig: 89 if array_inputs_bigwig:
86 all_datatype_dictionary['bigwig'] = array_inputs_bigwig 90 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
87 if array_inputs_gff3: 91 if array_inputs_gff3_transcript:
88 all_datatype_dictionary['gff3'] = array_inputs_gff3 92 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
93 if array_inputs_gff3_mrna:
94 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
89 if array_inputs_gtf: 95 if array_inputs_gtf:
90 all_datatype_dictionary['gtf'] = array_inputs_gtf 96 all_datatype_dictionary['gtf'] = array_inputs_gtf
91 if array_inputs_blastxml: 97 if array_inputs_blastxml:
92 all_datatype_dictionary['blastxml'] = array_inputs_blastxml 98 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
93 99