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bp_fastam9_to_table.1p

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

Comand 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