fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
DESCRIPTIONCommand 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
AUTHOR - Jason StajichJason Stajich jason_at_bioperl-dot-org