Summary

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

Package variables

Included modules

Inherit

Exporter

Synopsis

  use G::Tools::COGs;
  blah blah blah

Description

Stub documentation for G::Tools::COGs 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 cognitor {

    require LWP::UserAgent;

    opt_default(hit=>3);
    my @args = opt_get(@_);
    my $gb = opt_as_gb(shift @args);
    my $hit = opt_val("hit");

    my $ua = LWP::UserAgent->new();
    my $req = POST 'http://www.ncbi.nlm.nih.gov/COG/old/xognitor.cgi',
    [seq=>$gb->{SEQ}, hit=>$hit];
    my $content = $ua->request($req)->as_string;

    if ($content =~ /NO related COG/){
	#return '';
    }elsif($content =~ /<table/){
	$content =~ s/\///g;
	my (undef, $line, $undef) = split(/table/, $content, 3);
	substr($line, 0, 1) = '<';
	$line =~ s/<.*?>/ /g;
	my (undef, @lines) = split(/\n/, $line);
	
	my $i = 0;
	foreach (@lines){
	    s/^\s*//g;
	    s/\s*$//g;
	    if (/(\d+)\s+proteins/){
		$lines[$i] = $1;
	    }elsif(/BeTs to\s+(\d+)\s+clades/){
		$lines[$i] = $1;
	    }elsif(/pet-score:\s+(\d+)/){
		$lines[$i] = $1;
	    }
	    
	    $i ++;
	}
	
	return ($lines[2], $lines[1], $lines[3], $lines[0], $lines[4], $lines[5]);
	#       COGID      FUNCTION   PRODUCT    HITS       BeTs       pet-score
    }

}

sub dignitor {

    my $id = time . '-' . int(rand() * 100000);

    open(DIG, '>/tmp/dignitor-' . $id . '.lst');
    my $gene = shift;
    my $translation = shift;

    open(OUT, '>/tmp/in-' . $id . '.seq');
    print OUT "\>$gene\n$translation\n";
    close(OUT);
    
    my @result = _gblaster('-p blastp -d ' . $cogpath . 'COG/COGall -i /tmp/in-' . $id . '.seq -m8 -a 2');
    
    foreach my $tmp (@result){
	my ($query, $subject, $percent, $length, $qstart, $qend, $sstart, $send, 
	    $eval, $score) = @{$tmp};
	
	printf DIG "%s - %s (%d %s)  %d\.\.%d  %d\.\.%d\n", $query, $subject, $score, $eval,
	$qstart, $qend, $sstart, $send;
    }
    close(DIG);

    my $command = $cogpath . 'zugnitor /tmp/dignitor-' . $id . '.lst ' . $cogpath . 'COG/COGs.txt 2>/dev/null';
    my @result = `$command`;

    unlink('/tmp/dignitor-' . $id . '.lst');
    unlink('/tmp/in-' . $id . '.seq');
    my @coglist = ();
    foreach my $line (@result){
	last unless($line =~ /^\s/);

	if ($line =~ /(COG\d+)/){
	    push(@coglist, $1);
	}
    }

    if (wantarray()){
	return @coglist;
    }else{
	return shift @coglist;
    }

}

sub set_cogpath {

    $cogpath = shift;
    
    return $cogpath;

}

General documentation

Kazuharu Arakawa, gaou@sfc.keio.ac.jp

perl(1).