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comparison tools/ncbi_blast_plus/blastxml_to_tabular.py @ 23:31e517610e1f draft

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v0.3.0 Updated for NCBI BLAST+ 2.7.1
author peterjc
date Sat, 30 Jun 2018 17:22:46 -0400
parents 6f386c5dc4fb
children c877294f8025
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22:6f386c5dc4fb 23:31e517610e1f
106 Convert one (or more) BLAST XML files into a single tabular file. 106 Convert one (or more) BLAST XML files into a single tabular file.
107 107
108 The columns option can be 'std' (standard 12 columns), 'ext' 108 The columns option can be 'std' (standard 12 columns), 'ext'
109 (extended 25 columns), or a list of BLAST+ column names like 109 (extended 25 columns), or a list of BLAST+ column names like
110 'qseqid,sseqid,pident' (space or comma separated). 110 'qseqid,sseqid,pident' (space or comma separated).
111
112 Note if using a list of column names, currently ONLY the 25
113 extended column names are supported.
111 """ 114 """
112 parser = OptionParser(usage=usage) 115 parser = OptionParser(usage=usage)
113 parser.add_option('-o', '--output', dest='output', default=None, 116 parser.add_option('-o', '--output', dest='output', default=None,
114 help='output filename (defaults to stdout)', 117 help='output filename (defaults to stdout)',
115 metavar="FILE") 118 metavar="FILE")