Raw content of XrefParser::ncRNAParser
<![CDATA[package XrefParser::ncRNAParser;
use strict;
use POSIX qw(strftime);
use File::Basename;
use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: ncRNAParser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run($ARGV[0]);
}
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];
print "source_id = $source_id, species= $species_id, file = $file\n";
if(!defined($source_id)){
$source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
}
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
my %name_2_source_id=();
my $added=0;
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print STDERR "ERROR: Could not open file $file\n";
return 1;
}
while ( my $line = $file_io->getline() ) {
chomp $line;
my ($gene_id,$transcript_id,$source_name,$acc,$display_label,$full_description, $status)
= split("\t",$line);
#trim the description.
my ($description,$junk) = split("[[]Source:",$full_description);
if($source_name eq "miRNA_Registry"){
if($status eq "KNOWN"){
$source_name = "miRBase";
}
else{
$source_name = "miRBase_predicted";
}
}
if(!defined($name_2_source_id{$source_name})){
my $tmp = $self->get_source_id_for_source_name($source_name);
if(!$tmp){
die("Could not get source_id for $source_name\n");
}
$name_2_source_id{$source_name} = $tmp;
}
my $xref_id = $self->get_xref($acc,$name_2_source_id{$source_name}, $species_id);
if(!defined($xref_id)){
$xref_id = $self->add_xref($acc,"",$display_label,$description,$name_2_source_id{$source_name}, $species_id,"DIRECT");
$added++;
}
$self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));
#just add to the transcript ONLY as the check at the end will move all
#the those mapped to the transcript to the genes anyway due to the
#biomart check
# $self->add_direct_xref($xref_id, $gene_id, "Gene", "") if (defined($gene_id));
}
$file_io->close();
print "Added $added Xrefs for ncRNAs\n" if($verbose);
return 0;
}
1;
]]>