Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowse_hub.py @ 15:671231da45f9 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 594c5fa1e3cdb378ecf6b5490ec2cbac5fa8a61e-dirty
author yating-l
date Wed, 05 Jul 2017 15:47:15 -0400
parents 8d1cf7ce65cd
children
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14:f4a9197281d5 15:671231da45f9
45 # regtools (BED 12+1) 45 # regtools (BED 12+1)
46 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as') 46 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
47 47
48 # tblastn alignment (blastxml) 48 # tblastn alignment (blastxml)
49 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn') 49 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
50
51 # blat alignment (bigpsl 12+12)
52 parser.add_argument('--bigpsl', action='append', help='bigpsl format from blat alignment')
50 53
51 # BAM format 54 # BAM format
52 parser.add_argument('--bam', action='append', help='BAM format from HISAT') 55 parser.add_argument('--bam', action='append', help='BAM format from HISAT')
53 56
54 # BIGWIG format 57 # BIGWIG format
112 array_inputs_gff3 = args.gff3 115 array_inputs_gff3 = args.gff3
113 array_inputs_gff3_transcript = args.gff3_transcript 116 array_inputs_gff3_transcript = args.gff3_transcript
114 array_inputs_gff3_mrna = args.gff3_mrna 117 array_inputs_gff3_mrna = args.gff3_mrna
115 array_inputs_gtf = args.gtf 118 array_inputs_gtf = args.gtf
116 array_inputs_blastxml = args.blastxml 119 array_inputs_blastxml = args.blastxml
120 array_inputs_bigpsl = args.bigpsl
117 121
118 if array_inputs_bam: 122 if array_inputs_bam:
119 all_datatype_dictionary['bam'] = array_inputs_bam 123 all_datatype_dictionary['bam'] = array_inputs_bam
120 if array_inputs_bed: 124 if array_inputs_bed:
121 all_datatype_dictionary['bed'] = array_inputs_bed 125 all_datatype_dictionary['bed'] = array_inputs_bed
133 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna 137 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
134 if array_inputs_gtf: 138 if array_inputs_gtf:
135 all_datatype_dictionary['gtf'] = array_inputs_gtf 139 all_datatype_dictionary['gtf'] = array_inputs_gtf
136 if array_inputs_blastxml: 140 if array_inputs_blastxml:
137 all_datatype_dictionary['blastxml'] = array_inputs_blastxml 141 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
138 142 if array_inputs_bigpsl:
143 all_datatype_dictionary['bigpsl'] = array_inputs_bigpsl
139 print "input tracks: \n", all_datatype_dictionary 144 print "input tracks: \n", all_datatype_dictionary
140 145
141 for datatype, inputfiles in all_datatype_dictionary.items(): 146 for datatype, inputfiles in all_datatype_dictionary.items():
142 try: 147 try:
143 if not inputfiles: 148 if not inputfiles: