Christopher Fields > BioPerl-1.6.921 > bp_hmmer_to_table

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Source   Latest Release: BioPerl-1.6.924

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

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