Raw content of XrefParser::VbDirectParser
<![CDATA[package XrefParser::VbDirectParser;
use strict;
use File::Basename;
use Bio::SeqIO;
use XrefParser::BaseParser;
use vars qw(@ISA);
@ISA = qw(XrefParser::BaseParser);
# OParser for FASTA-format probe mappings from Agilent
# >A_23_P253586
# CTGTCAGGATTCTAGAACTTCTAAAATTAAAGTTTGGGGAAATCAGTAGCTCTGATGAGA
# >A_23_P217507
# AGAAAGACGTTTTCCAACATGTAGAACTGCTTTTTAACTGGAGGAAAAATACTTCAGGAG
sub run {
my ($self, $file, $source_id, $species_id) = @_;
open (INFILE, "<$file");
my $i=0;
print STDERR "source: ".$source_id."\tspecies: ".$species_id."\n";
my $type = "transcript";
while (my $ln = <INFILE>) {
chomp($ln);
my ($probe,$id, $version, $description, $ensembl_id) = split("\t",$ln);
$i++;
my $xref_id = XrefParser::BaseParser->get_xref($probe, $source_id, $species_id);
if (!defined($xref_id) || $xref_id eq "") {
$xref_id = XrefParser::BaseParser->add_xref($probe, 1, $probe, $description, $source_id, $species_id, "DIRECT");
}
XrefParser::BaseParser->add_direct_xref($xref_id, $ensembl_id, $type, $probe);
}
print $i." VB direct xrefs succesfully parsed\n" if($verbose);
close(INFILE);
return 0;
}
sub new {
my $self = {};
bless $self, "XrefParser::VbDirectParser";
return $self;
}
1;
]]>