Summary

G::Tools::GOA - Perl extension for blah blah blah

Package variables

Included modules

Inherit

AutoLoader Exporter

Synopsis

  use G::Tools::PBS;
  blah blah blah

Description

Stub documentation for G::Tools::GOA was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.

Methods

Methods description

None available.

Methods code

sub DESTROY {

    my $self = shift;

}

sub gopac {

    my $gb = shift;
    my $gopac = shift;
    my $n = 0;

    my $id = $gb->{CDS1}->{feature};
    unless (length($gb->{"FEATURE$id"}->{gopac})){
        set_goa($gb);
    }

    foreach my $cds ($gb->cds('all')){
	if ($gb->{$cds}->{gopac} =~ /$gopac/){
	    $gb->{$cds}->{on} = 1;
	    $n ++;
	}else{
	    $gb->{$cds}->{on} = 0;
	}
    }

    return $n;

}

sub read_goa {

    my $goa = {};
    my $path = shift;
    $path ||= '/db/genesys/sprot/gene_association.goa_sptr';
    my $n = 0;
    my %codeorder = (IEA=>1, NAS=>2, ISS=>3, IEP=>3,
		     IMP=>4, IGI=>4, IPI=>4, TAS=>5,
		     IDA=>5);

    open(FILE, $path) || die($!);
    while(<FILE>){
	chomp;
	my (undef, $id, $entry, undef, $go, undef, $evidence, undef, $aspect,
	    undef, undef, undef, undef, $date, undef) = split(/\t/, $_, 15);
	$n ++;
	print STDERR "." if ($n %100000 == 0);

	my $i = 1;
	my $flag = 0;
	while(1){
	    if($goa->{$id}->{$aspect}->{$i}->{GO}){
		if($goa->{$id}->{$aspect}->{$i}->{GO} eq $go){
		    if($codeorder{$goa->{$id}->{$aspect}->{$i}->{evidence}} <
		       $codeorder{$evidence})
		    {
			$goa->{$id}->{$aspect}->{$i}->{GO} = $go;
			$goa->{$id}->{$aspect}->{$i}->{evidence} = $evidence;
			$goa->{$id}->{$aspect}->{$i}->{date} = $date;
			$goa->{$id}->{$aspect}->{$i}->{entry} = $entry;
		    }
		    $flag = 1;
		    last;
		}else{
		    $i ++;
		}
	    }else{
		last;
	    }
	}
	next if ($flag);
	
	$goa->{$id}->{$aspect}->{$i}->{GO} = $go;
	$goa->{$id}->{$aspect}->{$i}->{evidence} = $evidence;
	$goa->{$id}->{$aspect}->{$i}->{date} = $date;
	$goa->{$id}->{$aspect}->{$i}->{entry} = $entry;
    }
    close(FILE);
    
    print STDERR "\n";

    return $goa;

}

sub set_goa {

    my $gb = shift;
    my $path = shift || '';
    my $goa = read_goa($path);
    my %codeorder = (IEA=>1, NAS=>2, ISS=>3, IEP=>3,
		     IMP=>4, IGI=>4, IPI=>4, TAS=>5,
		     IDA=>5);

    print STDERR "loaded GOA...\n";

    if ($gb->filepath() =~ /\.embl$/){
	foreach my $cds ($gb->cds()){
	    my $xref = $gb->{$cds}->{db_xref};
	    my $id;
	    if ($xref =~ /SWISS-PROT\:(.*)/ || $xref =~ /UniProt\/TrEMBL:(.*)/){
		$id = $1;
		
		if ($goa->{$id}){
		    my %goanum = (0=>1);
		    foreach my $aspect (keys %{$goa->{$id}}){
			foreach my $i (keys %{$goa->{$id}->{$aspect}}){
			    $gb->{$cds}->{"GO:$aspect"} .= 
				$goa->{$id}->{$aspect}->{$i}->{GO} . ";";
			    $gb->{$cds}->{"GO:$aspect:evidence"} .=
				$goa->{$id}->{$aspect}->{$i}->{evidence} . ";";
			    $goanum{$codeorder{$goa->{$id}->{$aspect}->{$i}->{evidence}}}++;
			}
		    }
		    $gb->{$cds}->{gopac} = join('', (sort keys %goanum));
		}
	    }
	}
    }

}

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).