NAME

bp_hmmer_to_table - turn HMMER output into tabular format

SYNOPSIS

 bp_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