bp_fastam9_to_tablep - Online in the Cloud

PROGRAM:

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

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