Raw content of XrefParser::IlluminaWGParser
<![CDATA[package XrefParser::IlluminaWGParser;
use strict;
use base qw( XrefParser::BaseParser );
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 @xrefs;
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print STDERR "Could not open $file\n";
return 1;
}
my $read = 0;
my $name_index;
my $seq_index;
my $defin_index;
while ( $_ = $file_io->getline() ) {
chomp;
my $xref;
# strip ^M at end of line
$_ =~ s/\015//g;
if(/^\[/){
# print $_."\n";
if(/^\[Probes/){
my $header = $file_io->getline();
# print $header."\n";
$read =1;
my @bits = split("\t", $header);
my $index =0;
foreach my $head (@bits){
if($head eq "Search_Key"){
$name_index = $index;
}
elsif($head eq "Probe_Sequence"){
$seq_index = $index;
}
elsif($head eq "Definition"){
$defin_index = $index;
}
$index++;
}
if(!defined($name_index) or !defined($seq_index) or !defined($defin_index)){
die "Could not find index for search_key->$name_index, seq->$seq_index, definition->$defin_index";
}
next;
}
else{
$read = 0;
}
}
if($read){
# print $_."\n";
my @bits = split("\t", $_);
my $sequence = $bits[$seq_index];
my $description = $bits[$defin_index];
my $illumina_id = $bits[$name_index];
# build the xref object and store it
$xref->{ACCESSION} = $illumina_id;
$xref->{LABEL} = $illumina_id;
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{DESCRIPTION} = $description;
$xref->{SEQUENCE_TYPE} = 'dna';
$xref->{STATUS} = 'experimental';
push @xrefs, $xref;
}
}
$file_io->close();
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
print scalar(@xrefs) . " Illumina V2 xrefs succesfully parsed\n" if($verbose);
return 0;
}
1;
]]>