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Manual Reference Pages  -  BP_FASTAM9_TO_TABLE.PL (1)

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NAME

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

CONTENTS

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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