Christopher Fields > BioPerl-1.6.923 > fastm9_to_table

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Source   Latest Release: BioPerl-1.6.924

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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