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