Raw content of XrefParser::HPAParser
<![CDATA[package XrefParser::HPAParser;
use strict;
use base qw( XrefParser::BaseParser);
# This parser will read direct xrefs from a simple comma-delimited file downloaded from the Human Protein Atlas (HPA) database.
# The database contains two types of antibody, their own HPA antibodies and Collaborator antibody (CAB) commercial antibodies.
# The columns of the file should be the following:
#
# 1) Antibody
# 2) Antibody ID
# 3) Ensembl Peptide ID
# 4) Link (URL)
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $rel_url = shift;
my $verbose = shift;
my $filename = @{$files}[0];
my $file_io = $self->get_filehandle($filename);
if ( !defined($file_io) ) {
return 1;
}
my $parsed_count = 0;
$file_io->getline();
while ( defined( my $line = $file_io->getline() ) ) {
$line =~ s/\s*$//;
my ( $antibody, $antibody_id, $ensembl_peptide_id, $link) = split( /,/, $line );
if ( !defined($antibody) || !defined($ensembl_peptide_id) ) {
printf( "Line %d contains has less than two columns.\n",
1 + $parsed_count );
print ("The parsing failed\n");
return 1;
}
my $label = $antibody;
my $type = 'translation';
my $description = '';
my $version = '1';
++$parsed_count;
my $xref_id = XrefParser::BaseParser->get_xref( $antibody_id, $source_id, $species_id );
if ( !defined($xref_id) || $xref_id eq '' ) {
$xref_id = XrefParser::BaseParser->add_xref($antibody_id, $version, $label, $description, $source_id, $species_id, "DIRECT");
}
XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_peptide_id, $type, '');
} ## end while ( defined( my $line...
printf( "%d direct xrefs succesfully parsed\n", $parsed_count ) if($verbose);
$file_io->close();
return 0;
} ## end sub run
1;
]]>