Mercurial > repos > yating-l > jbrowse_hub

comparison jbrowse_hub.py @ 50:3e5b6f6a9abe draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty
author yating-l
date Thu, 30 Mar 2017 16:03:16 -0400
parents a5108e5010b4
children ed17bb465bde
comparison
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49:193e94a43f0f 50:3e5b6f6a9abe
25 parser.add_argument('-e', '--extra_files_path', help='Directory of JBrowse Hub folder') 25 parser.add_argument('-e', '--extra_files_path', help='Directory of JBrowse Hub folder')
26 26
27 #Tool Directory 27 #Tool Directory
28 parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools') 28 parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools')
29 29
30 #GFF3
31 parser.add_argument('--gff3', action='append', help='GFF3 format')
32
30 # GFF3 structure: gene->transcription->CDS 33 # GFF3 structure: gene->transcription->CDS
31 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS') 34 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format for gene prediction, structure: gene->transcription->CDS')
32 35
33 # GFF3 structure: gene->mRNA->CDS 36 # GFF3 structure: gene->mRNA->CDS
34 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS') 37 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format for gene prediction, structure: gene->mRNA->CDS')
38
39 # generic BED
40 parser.add_argument('--bed', action='append', help='BED format')
35 41
36 # trfBig simple repeats (BED 4+12) 42 # trfBig simple repeats (BED 4+12)
37 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as') 43 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
38 44
39 # regtools (BED 12+1) 45 # regtools (BED 12+1)
91 97
92 #Initate trackObject 98 #Initate trackObject
93 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) 99 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path)
94 100
95 array_inputs_bam = args.bam 101 array_inputs_bam = args.bam
102 array_inputs_bed = args.bed
96 array_inputs_bed_simple_repeats = args.bedSimpleRepeats 103 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
97 array_inputs_bed_splice_junctions = args.bedSpliceJunctions 104 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
98 array_inputs_bigwig = args.bigwig 105 array_inputs_bigwig = args.bigwig
106 array_inputs_gff3 = args.gff3
99 array_inputs_gff3_transcript = args.gff3_transcript 107 array_inputs_gff3_transcript = args.gff3_transcript
100 array_inputs_gff3_mrna = args.gff3_mrna 108 array_inputs_gff3_mrna = args.gff3_mrna
101 array_inputs_gtf = args.gtf 109 array_inputs_gtf = args.gtf
102 array_inputs_blastxml = args.blastxml 110 array_inputs_blastxml = args.blastxml
103 111
104 if array_inputs_bam: 112 if array_inputs_bam:
105 all_datatype_dictionary['bam'] = array_inputs_bam 113 all_datatype_dictionary['bam'] = array_inputs_bam
114 if array_inputs_bed:
115 all_datatype_dictionary['bed'] = array_inputs_bed
106 if array_inputs_bed_simple_repeats: 116 if array_inputs_bed_simple_repeats:
107 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats 117 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
108 if array_inputs_bed_splice_junctions: 118 if array_inputs_bed_splice_junctions:
109 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions 119 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
110 if array_inputs_bigwig: 120 if array_inputs_bigwig:
111 all_datatype_dictionary['bigwig'] = array_inputs_bigwig 121 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
122 if array_inputs_gff3:
123 all_datatype_dictionary['gff3'] = array_inputs_gff3
112 if array_inputs_gff3_transcript: 124 if array_inputs_gff3_transcript:
113 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript 125 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
114 if array_inputs_gff3_mrna: 126 if array_inputs_gff3_mrna:
115 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna 127 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
116 if array_inputs_gtf: 128 if array_inputs_gtf: