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BP_FASTAM9_TO_TABLE(1)                     User Contributed Perl Documentation

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 v5.20.2                      2015-09-15            BP_FASTAM9_TO_TABLE(1)