bp_hmmer_to_table.pl

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

hmmer_to_table - turn HMMER output into tabular format

SYNOPSIS

  hmmer_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.

   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