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# $Id: mesh_parser.pm,v 1.4 2005/03/30 21:15:48 cmungall Exp $
#
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::Parsers::mesh_parser;
=head1 NAME
GO::Parsers::mesh_parser - Parses Mesh ascii text files
=head1 SYNOPSIS
do not use this class directly; use GO::Parser
=cut
=head1 DESCRIPTION
EXPERIMENTAL
=head1 AUTHOR
=cut
use Exporter;
use GO::Parsers::base_parser;
@ISA = qw(GO::Parsers::base_parser Exporter);
use Carp;
use FileHandle;
use strict qw(subs vars refs);
sub parse_file {
my ($self, $file, $dtype) = @_;
$self->file($file);
my $fh = new FileHandle($file);
if (!$fh) {confess "Couldn't open '$file': $!"};
$/ = '*NEWRECORD';
my %treenode2acc = ();
$self->start_event("subgraph");
my @accs = ();
my $lnum = 0;
PARSELINE:
while (my $block = <$fh>) {
chomp $block;
next unless $block;
++$lnum;
$self->line($block);
$self->line_no($lnum);
my @lines = split(/\n/, $block);
my ($name, $acc, $def, @mn);
map {
if (/(\w+) = (.*)/) {
my ($key, $val) = ($1, $2);
if ($key eq "MH") {
$name = $val;
}
if ($key eq "UI") {
$acc = $val;
}
if ($key eq "MS") {
$def = $val;
}
if ($key eq "MN") {
push(@mn, $val);
}
}
} @lines;
$self->event('term',
[
[name=>$name],
[acc=>"Mesh:$acc"],
[term_type=>"Mesh"],
]
);
$self->event('def',
[
['godef-goid'=>$acc],
['godef-definition'=>$def],
]
) if $def;
push(@accs, $acc);
foreach (@mn) {
$treenode2acc{$_} = $acc;
}
}
foreach my $tn (keys %treenode2acc) {
my $child = $treenode2acc{$tn};
my $pn = $tn;
$pn =~ s/\.(\d+)$//;
if ($pn ne $tn) {
my $parent = $treenode2acc{$pn};
$self->event("term" => [
[acc=>$child],
[rel=> [
[type => 'isa'],
[obj=>$parent]
]
]
]
);
}
}
$self->end_event("subgraph");
$self->parsed_ontology(1);
# use Data::Dumper;
# print Dumper $self;
}
1;
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