cmzmasek

<?xml version="1.0"?>
<rdf:RDF
 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
 xmlns:hmmer_hit="http://www.open-bio.org/core/hmmer_hit/"
>
    <rdf:Description rdf:about="http://pfam.sanger.ac.uk/family?acc=PF00400.26">
            <hmmer_hit:target_name>WD40</hmmer_hit:target_name>
            <hmmer_hit:query_name>sp|O14727|APAF_HUMAN</hmmer_hit:query_name>
            <hmmer_hit:full_sequence_e_value>2.0e-82</hmmer_hit:full_sequence_e_value>
            <hmmer_hit:full_sequence_score>268.1</hmmer_hit:full_sequence_score>

cmzmasek

<?xml version="1.0"?>
<rdf:RDF
 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
 xmlns:hmmer_hit="http://www.open-bio.org/core/hmmer_hit/"
>
    <rdf:Description rdf:about="http://pfam.sanger.ac.uk/family?acc=PF00400.26">
            <hmmer_hit:target_name>WD40</hmmer_hit:target_name>
            <hmmer_hit:target_length>39</hmmer_hit:target_length>
            <hmmer_hit:query_name>sp|O14727|APAF_HUMAN</hmmer_hit:query_name>
            <hmmer_hit:query_length>1248</hmmer_hit:query_length>

cmzmasek

#!/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