SYNOPSIS

hmmer_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.

  query sequence/domain (these are flip-flopped for hmmsearch / hmmpfam)  
  query start
  query end
  domain/sequence name or PFAM accession 
  hit start
  hit end
  score
  e-value
  domain/sequence name (these are flip-flopped for hmmsearch / hmmpfam)

AUTHOR - Jason Stajich

Jason Stajich jason_at_bioperl-dot-org