Example for HMMER3 support in BioRuby and RDf/XML output

bioruby_hmmer_rdfxml

#!/usr/bin/env ruby
# code is currently at: https://github.com/cmzmasek/bioruby/tree/master/lib/bio/
# launch with (by way of example): ruby -I ~/MY_BIORUBY/bioruby/lib/ hmmer_02.rb
require 'bio'
factory = Bio::HMMER3.new('/home/zma/SOFTWARE/hmmer-3.0/src/hmmscan',
                          '/home/zma/DATA/PFAM/PFAM25/Pfam-A.hmm',
                          '/home/zma/SOFTWARE_DEV/bioruby_hmmer/APAF_HUMAN.fasta',
                          '--domtblout' )
puts factory.options
report = factory.query
puts report.to_rdf

puts

factory = Bio::HMMER3.new('/home/zma/SOFTWARE/hmmer-3.0/src/hmmscan',
                          '/home/zma/DATA/PFAM/PFAM25/Pfam-A.hmm',
                          '/home/zma/SOFTWARE_DEV/bioruby_hmmer/APAF_HUMAN.fasta',
                          '--tblout' )
puts factory.options
puts report.to_rdf