fastm9_to_table(1) turn FASTA -m 9 output into NCBI -m 9 tabular output


fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...


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.

 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 
 bit score

Additionally 3 more columns are provided
 fasta score
 percent similar
 query length
 hit length
 query gaps
 hit gaps

AUTHOR - Jason Stajich

Jason Stajich jason_at_bioperl-dot-org