GramenePathwayParser.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
package XrefParser::GramenePathwayParser;
 
=pod
 
=head1 NAME
 
XrefParser::GramenePathwayParser
 
=head1 DESCRIPTION
 
Parse pathway dumps from Gramene.  File format (and example data):
 
 gene_name                  AT1G66030
 enzyme_name                fatty acid (omega-1)-hydroxylase
 reaction_id                RXN-7796
 reaction_name              
 ec                         2.7.7.-
 pathway_id                 PWY-5129
 pathway_name               sphingolipid biosynthesis (plants)
 
=head1 AUTHOR
 
Ken Youens-Clark E<lt>kclark@cshl.eduE<gt>.
 
=cut
 
use strict;
use Text::RecordParser::Tab;
use base 'XrefParser::BaseParser';
 
sub run {
    my ($self, $args) = @_;
    my $source_id     = $args->{'source_id'};
    my $species_id    = $args->{'species_id'};
    my $files         = $args->{'files'};
    my $release_file  = $args->{'rel_file'};
    my $verbose       = $args->{'verbose'};
    my $file          = ref $files eq 'ARRAY' ? shift @$files : '';
 
    if ( !$file ) {
        printf STDERR "%s called without a 'files' argument\n%s", 
            __PACKAGE__, Dumper($args);
        return 1; # error
    }
 
    my $p = Text::RecordParser::Tab->new( $file );
 
    my $direct_xref_count = 0;
    while ( my $rec = $p->fetchrow_hashref ) {
        my $gene = $rec->{'gene_name'} or next;
 
        if ( my $ec = $rec->{'ec'} ) {
            my $ec_xref_id = $self->add_xref({
                source_id  => $source_id,
                species_id => $species_id,
                acc        => $ec,
                label      => '',
                desc       => '',
                info_type  => 'DIRECT',
            });
 
            $self->add_direct_xref( $ec_xref_id, $gene, 'Gene', 'DIRECT' );
            $direct_xref_count++;
        }
 
        if ( my $pathway_id = $rec->{'pathway_id'} ) {
            my $pathway_xref_id = $self->add_xref({
                source_id  => $source_id,
                species_id => $species_id,
                acc        => $pathway_id,
                label      => $rec->{'pathway_name'},
                desc       => '',
                info_type  => 'DIRECT'
            });
 
            $self->add_direct_xref( $pathway_xref_id, $gene, 'Gene', 'DIRECT' );
            $direct_xref_count++;
        }
    }
 
    printf "Parsed pathway Ids from file '%s,' added %s direct_xrefs\n",
        $file, $direct_xref_count;
 
    return 0; # success
}
 
1;