debian man page for bp_fastam9_to_table

BP_FASTAM9_TO_TABLE(1p) 				User Contributed Perl Documentation				   BP_FASTAM9_TO_TABLE(1p)

NAME
       fastm9_to_table	- turn FASTA -m 9 output into NCBI -m 9 tabular output

SYNOPSIS
	fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...

DESCRIPTION
       Command line options:
	 -e/--evalue   evalue	 -- filter by evalue
	 -b/--bitscore bitscore  -- filter by bitscore
	 --header		 -- boolean flag to print column header
	 -o/--out		 -- optional outputfile to write data,
				    otherwise will write to STDOUT
	 -h/--help		 -- show this documentation

       Not technically a SearchIO script as this doesn't use any Bioperl components but is a useful and fast.  The output is tabular output with
       the standard NCBI -m9 columns.

	queryname
	hit name
	percent identity
	alignment length
	number mismatches
	number gaps
	query start  (if on rev-strand start > end)
	query end
	hit start (if on rev-strand start > end)
	hit end
	evalue
	bit score

       Additionally 3 more columns are provided
	fasta score
	sw-score
	percent similar
	query length
	hit length
	query gaps
	hit gaps

AUTHOR - Jason Stajich
       Jason Stajich jason_at_bioperl-dot-org

perl v5.14.2							    2012-03-02						   BP_FASTAM9_TO_TABLE(1p)