Raw content of XrefParser::CoordinateParser
<![CDATA[# $Id: CoordinateParser.pm,v 1.2 2007/11/06 12:25:47 ak4 Exp $
# This sub-class of XrefParser::BaseParser serves as the parent class
# for parsers of Xref source data that we use coordinate overlap to
# determine the Xrefs to.
package XrefParser::CoordinateParser;
use strict;
use warnings;
use Carp;
use base qw( XrefParser::BaseParser );
our $add_xref_sth;
our $add_xref_sql = q(
INSERT INTO coordinate_xref
( source_id, species_id,
accession,
chromosome, strand,
txStart, txEnd,
cdsStart, cdsEnd,
exonStarts, exonEnds )
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
);
sub add_xref {
my $self = shift;
my ( $source_id, $species_id, $xref ) = @_;
if ( !defined($add_xref_sth) ) {
my $dbh = $self->dbi();
$add_xref_sth = $dbh->prepare_cached($add_xref_sql);
if ( !defined($add_xref_sth) ) {
croak( $dbh->errstr() );
}
}
for my $required_key ( 'accession', 'chromosome',
'strand', 'txStart',
'txEnd', 'exonStarts',
'exonEnds' )
{
if ( !defined( $xref->{$required_key} ) ) {
croak(
sprintf( "Missing required key '%s' for Xref", $required_key )
);
}
}
$add_xref_sth->execute( $source_id, $species_id,
$xref->{'accession'}, $xref->{'chromosome'},
$xref->{'strand'}, $xref->{'txStart'},
$xref->{'txEnd'}, $xref->{'cdsStart'},
$xref->{'cdsEnd'}, $xref->{'exonStarts'},
$xref->{'exonEnds'}
) or croak( $add_xref_sth->errstr() );
}
1;
]]>