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# $Id: go_xref_parser.pm,v 1.9 2010/02/15 17:34:57 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::go_xref_parser;
=head1 NAME
GO::Parsers::go_xref_parser - syntax parsing of GO xref flat files (eg eg2go, metacyc2go)
=head1 SYNOPSIS
do not use this class directly; use GO::Parser
=cut
=head1 DESCRIPTION
This generates Stag event streams from one of the various GO flat file
formats (ontology, defs, xref, associations). See GO::Parser for details
Examples of these files can be found at http://www.geneontology.org
A description of the event streams generated follows; Stag or an XML
handler can be used to catch these events
=head1 GO XREF FILES
These files have a filename *2go; eg metacyc2go
(dbxrefs
(termdbxref+
(termacc "s")
(dbxref
(xref_dbname "s")
(xref_key "s"))))
=head1 AUTHOR
=cut
use Carp;
use FileHandle;
use strict qw(vars refs);
use base qw(GO::Parsers::base_parser);
use GO::Parsers::ParserEventNames; # XML constants
sub dtd {
'go_xref-parser-events.dtd';
}
sub parse_fh {
my ($self, $fh) = @_;
my $file = $self->file;
my $lnum = 0;
$self->start_event(OBO);
while (<$fh>) {
chomp;
tr [\200-\377]
[\000-\177]; # see 'man perlop', section on tr/
# weird ascii characters should be excluded
tr/\0-\10//d; # remove weird characters; ascii 0-8
# preserve \11 (9 - tab) and \12 (10-linefeed)
tr/\13\14//d; # remove weird characters; 11,12
# preserve \15 (13 - carriage return)
tr/\16-\37//d; # remove 14-31 (all rest before space)
tr/\177//d; # remove DEL character
$lnum++;
next if /^\!/;
next if /^$/;
$self->line($_);
$self->line_no($lnum);
my ($ext, @goids) = split(' > ',$_);
if ($ext =~ /^([\w\-]+):?(\S+)(.*)/) {
my ($db,$dbacc,$name) = ($1,$2,$3);
$name =~ s/^\s+// if $name;
$dbacc =~ s/\s/\%20/g;
foreach my $goid (@goids) {
if ($goid =~ /(.*)\s+\;\s+(.*)/) {
my $goacc = $2;
if ($self->acc_not_found($goacc)) {
$self->parse_err("No such ID: $goacc");
next;
}
$self->start_event(TERM);
$self->event(ID, $goacc);
$self->start_event(XREF_ANALOG);
$self->event(ACC, $dbacc);
$self->event(DBNAME, $db);
if ($name) {
$self->event(NAME, $name)
}
$self->end_event(XREF_ANALOG);
$self->end_event(TERM);
}
else {
$self->parse_err("would not extract GO ID from: $goid");
}
}
}
else {
$self->parse_err("bad external ID: $ext in line: $_");
}
}
$self->end_event(OBO);
}
1;
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