Raw content of XrefParser::WormPepParser
<![CDATA[package XrefParser::WormPepParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
# wormpep.table file format:
#>B0025.1a CE24759 vps-34 phosphatidylinositol 3-kinase Confirmed SW:Q9TXI7 AAF23184.1
#>B0025.1b CE24760 vps-34 Confirmed SW:Q9TXI6 AAF23185.1
#>B0025.1c CE37691 vps-34 Confirmed SW:Q5TYK9 AAV34807.1
# Just need direct xref between B0025.1a (=stable ID for C. Elegans) and CE24759
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $release_file = shift;
my $verbose = shift;
my $file = @{$files}[0];
my $worm_source_id = XrefParser::BaseParser->get_source_id_for_source_name('wormpep_id');
my $worm_locus_id = XrefParser::BaseParser->get_source_id_for_source_name('wormbase_locus');
my $xref_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$worm_source_id AND species_id=$species_id");
my $xref_sth2 = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$worm_locus_id AND species_id=$species_id");
my $pep_io = $self->get_filehandle($file);
if ( !defined $pep_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 error
}
my ($x_count, $d_count);
while ( $_ = $pep_io->getline() ) {
my ($transcript, $wb, $display) = (split(/\t/,substr($_,1)))[0,1,2];
# reuse or create xref
$xref_sth->execute($wb);
my $xref_id = ($xref_sth->fetchrow_array())[0];
if (!$xref_id) {
$xref_id = $self->add_xref($wb, undef, $wb, "", $worm_source_id, $species_id);
$x_count++;
}
# and direct xref
$self->add_direct_xref($xref_id, $transcript, "transcript", "");
$d_count++;
if(defined($display) and length($display) > 0 ){
$xref_sth2->execute($display);
my $xref_id2 = ($xref_sth2->fetchrow_array())[0];
if (!$xref_id2) {
$xref_id2 = $self->add_xref($display, undef, $display, "", $worm_locus_id, $species_id);
$x_count++;
}
# and direct xref
$self->add_direct_xref($xref_id2, $transcript, "transcript", "");
}
$d_count++;
}
$pep_io->close();
print "Added $d_count direct xrefs and $x_count xrefs\n" if($verbose);
return 0;
}
1;
]]>