G::Seq::Util - Miscellaneous analysis methods related to sequence analysis.

    This class is a part of G-language Genome Analysis Environment, 
    collecting miscellaneous sequence analysis methods.

    opt_default(upstream=>50, downstream=>50, codon=>"atg");
    my @args = opt_get(@_);
    my $gb = opt_as_gb(shift @args);

    my $upstream = int(opt_val("upstream") / 3);
    my $downstream = int(opt_val("downstream") / 3);
    my $codon = opt_val("codon");
    die ("codon must be 3 letters") if (length($codon) != 3);

    foreach my $cds ($gb->cds()){
	my $seq = $gb->around_startcodon($cds, $upstream * 3, $downstream * 3, "without");

	for(my $j = 0; $j <= length($seq) - 3; $j +=3){
	    if(substr($seq, $j, 3) eq $codon){
		$gb->{$cds}->{on} = 0;
		last;
	    }
	}
    }

    return $gb->cds();

    my $nuc=shift;
    my $gene='you have just found the king of genes.'."\n";
    
    system("wget http://www.stagnightout.com/pics/what-to-wear/21280.jpg -O /tmp/afro.jpg -q");
    msg_gimv('/tmp/afro.jpg');
    
    return $gene;

    my $num = shift || 8;

    local *transferase = sub{
	my @result;
	foreach my $key (@_){
	    push(@result, $key . $_) for (qw/a t g c/);
	}
	return @result;
    };

    my @result = ('');
    for (1..$num){
	@result = &transferase(@result);
    }
    return @result;

    my $this = opt_as_gb(shift @_);
    my $new = new G::IO("blessed");
    annotate_with_LORF($new, $this);

    return $new;

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

    my %mw = ("a", 313.15, "t", 304.19, "g", 329.19, "c", "289.13", "n", 308.915);
    my $i = 0;
    my $weight = 0;

    while(substr($gb->{SEQ}, $i, 1) ne ''){
	if (substr($gb->{SEQ}, $i, 1) =~ /[atgc]/){
	    $weight += $mw{substr($gb->{SEQ}, $i, 1)};
	}else{
	    $weight += $mw{"n"};
	}
	$i ++;
    }
    my $double = $weight * 2;

    msg_send(sprintf "  Molecular Weight of Nucleotides:\n");
    msg_send(sprintf "    single strand:  %12d\n",$weight); 
    msg_send(sprintf "    double strand:  %12d\n\n\n",$double); 

    $weight *= 2 if ($strand eq "double");


    return $weight;

    my @args = opt_get(@_);
    my $seq = shift @args;
    my $frame = shift @args;
    my $len = length($seq);
    if ($frame > 3){
	$seq = G::Seq::Util::complement($seq);
	$frame -= 3;
    }

    my %CodonTable = (
               'gac', 'D', 'caa', 'Q', 'gca', 'A', 'ctg', 'L',
               'gat', 'D', 'cag', 'Q', 'gcc', 'A', 'ctt', 'L',
               'gaa', 'E', 'agc', 'S', 'gcg', 'A', 'ata', 'I',
               'gag', 'E', 'agt', 'S', 'gct', 'A', 'atc', 'I',
               'aga', 'R', 'tca', 'S', 'gga', 'G', 'att', 'I',
               'agg', 'R', 'tcc', 'S', 'ggc', 'G', 'cca', 'P',
               'cga', 'R', 'tcg', 'S', 'ggg', 'G', 'ccc', 'P',
               'cgc', 'R', 'tct', 'S', 'ggt', 'G', 'ccg', 'P',
               'cgg', 'R', 'aca', 'T', 'gta', 'V', 'cct', 'P',
               'cgt', 'R', 'acc', 'T', 'gtc', 'V', 'atg', 'M',
               'aaa', 'K', 'acg', 'T', 'gtg', 'V', 'tgg', 'W',
               'aag', 'K', 'act', 'T', 'gtt', 'V', 'tgc', 'C',
               'cac', 'H', 'tac', 'Y', 'tta', 'L', 'tgt', 'C',
               'cat', 'H', 'tat', 'Y', 'ttg', 'L', 'taa', '/',
               'aac', 'N', 'ttc', 'F', 'cta', 'L', 'tag', '/',
               'aat', 'N', 'ttt', 'F', 'ctc', 'L', 'tga', '/'
                  );

    my $return = '';
    my $i;
    for ($i = 0; $i < $len; $i ++){
	if ($i < $frame - 1){
	    $return .= substr($seq, $i, $frame - 1) . '-';
	    $i += $frame - 2;
	} elsif ($i + 3 <= $len){
	    $return .= $CodonTable{substr($seq, $i, 3)};
	    $i += 2;
	    $return .= '-' unless ($i >= $len - 1);
	} else {
	    $return .= substr($seq, $i);
	    last;
	}
    }
    return $return;

    return opt_as_gb(shift @_)->seq_info(shift @_);

    opt_default(length=>100, filename=>"view_cds.png", 
		  gap=>3, output=>"show", application=>"gimv");
    my @args = opt_get(@_);
    my $gb = opt_as_gb(shift @args);
    my $data = {};
    my @pos;
    my $numcds = scalar $gb->cds();
    my $i = 0;
    my $gap = opt_val("gap");
    my $length = opt_val("length");
    my $filename = opt_val("filename");
    my $output = opt_val("output");
    my $application = opt_val("application");

    $filename = "view_cds.csv" if ($output eq "f" &&
				   opt_val("filename") eq "view_cds.png");
    for my $nuc (qw/a t g c/){
	for ($i = 0; $i < $length * 4 + 6 + $gap; $i++){
	    $data->{$nuc}->[i] = 0;
	}
    }

    foreach my $cds ($gb->cds()){
	my $seq = $gb->around_startcodon($cds, $length, $length);
	
	for ($i = 0; $i < length($seq); $i ++){
	    $data->{substr($seq, $i, 1)}->[$i] += 100/$numcds;
	}

	$seq  = $gb->around_stopcodon($cds, $length, $length);

	for ($i = 0; $i < length($seq); $i ++){
	    $data->{substr($seq, $i, 1)}->[$i + length($seq) + $gap] += 100/$numcds;
	}
    }
    
    for ($i = 1; $i <= $length * 4 + 6 + $gap; $i ++){
	push(@pos, $i);
    }

    if ($output eq "g" || $output eq "show"){
	_UniMultiGrapher(\@
			 pos, -x => "position", -y => "percentage",
			 [@{$data->{a}}], [@{$data->{t}}], [@{$data->{g}}], [@{$data->{c}}],
			 -x1=>"A", -x2=>"T",
			 -x3=>"G", -x4=>"C",
			 -filename => $filename,
			 -title => "Base Contents Around Start/Stop Codons"
			 );
	msg_gimv("graph/$filename") if($output eq "show");
    }elsif ($output eq "f"){
	open(OUT, '>data/' . $filename);
	print OUT "position,A,T,G,C\n";
	
	for ($i = 0; $i < $length * 4 + 6 + $gap; $i ++){
	    printf OUT "%d,%3.2f,%3.2f,%3.2f,%3.2f\n", $i + 1, 
	    $a[$i], $t[$i], $g[$i], $c[$i];
	}
	close(OUT);
    }