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BP_FASTAM9_TO_TABLE(1)User Contributed Perl DocumentatioBP_FASTAM9_TO_TABLE(1)

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 v5.24.1			  2017-07-08		BP_FASTAM9_TO_TABLE(1)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR - Jason Stajich

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<https://www.freebsd.org/cgi/man.cgi?query=bp_fastam9_to_table.pl&sektion=1&manpath=FreeBSD+12.0-RELEASE+and+Ports>

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