sub circular_map
{ opt_default("gmap"=>1, "filename"=>"circular_map.svg", "output"=>"g");
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $filename = opt_val("filename");
my $gmap = opt_val("gmap");
my $optionalText = opt_val("optionalText");
mkdir( "data", 0777 );
mkdir( "graph", 0777 );
msg_error("Map generation will take a few minutes. Please make yourself comfortable until the image is generated ;-\)\n\n") if ($gmap);
my $wfile = $gb->{LOCUS}->{id};
my ( $ori, $ter ) = find_ori_ter( $gb, -output => "/dev/null" );
my $bp_length = int(length( $gb->{SEQ} ));
my ( $count_a, $count_b );
my $svg = SVG->new(
width => $cx * 2,
height => $cy * 2,
'xmlns:xlink' => 'http://www.w3.org/1999/xlink'
);
my $tag = $svg->rect(
width => $cx * 2,
height => $cy * 2,
x => 0,
y => 0,
fill => 'black'
);
my $y = $svg->group(
id => 'group_y',
style =>
{ 'stroke' => '#ff9966', 'fill' => 'none', 'stroke-width' => 200 }
);
$svg->circle(
id => "cdsringbackground",
cx => $cx,
cy => $cy,
r => 3250,
'stroke' => '#222222',
'opacity' => 0.8,
'fill' => 'none',
'stroke-width' => 500
);
my $ry = $cy - 3250;
if($gb->{LOCUS}->{circular} == 0){
my $r = 3550;
my ( $rx, $ry2 ) = &get_pos( int(length($gb->{SEQ}) * 47/48), $r, $bp_length );
$svg->polygon(
points=>"$cx,$ry $rx,$ry2 $cx,$ry2",
stroke=>"#000000",
fill=>'#000000',
'stroke-width'=>30
);
$r = 2950;
( $rx, $ry2 ) = &get_pos( int(length($gb->{SEQ}) * 47/48), $r, $bp_length );
$svg->polygon(
points=>"$cx,$ry $rx,$ry2 $cx,$ry2",
stroke=>"#000000",
fill=>'#000000',
'stroke-width'=>30
);
}
my $scla = $svg->group(
id => 'scale_a',
style =>
{ 'stroke' => '#333333', 'fill' => 'none', 'stroke-width' => 1 }
);
my $sclb = $svg->group(
id => 'scale_b',
style =>
{ 'stroke' => '#ffffff', 'fill' => 'none', 'stroke-width' => 2 }
);
my $sclc = $svg->group(
id => 'scale_c',
style =>
{ 'stroke' => '#ffffff', 'fill' => 'none', 'stroke-width' => 2 }
);
my $cdsa = $svg->group(
id => 'cds_a',
style =>
{ 'stroke' => '#cc0066', 'fill' => 'none', 'stroke-width' => 300 }
);
my $cdsb = $svg->group(
id => 'cds_b',
style =>
{ 'stroke' => '#cc0033', 'fill' => 'none', 'stroke-width' => 300 }
);
my $cdsx = $svg->group(
id => 'cds_x',
style =>
{ 'stroke' => '#ccff33', 'fill' => 'none', 'stroke-width' => 300 }
);
my $cdsy = $svg->group(
id => 'cds_y',
style =>
{ 'stroke' => '#99cc00', 'fill' => 'none', 'stroke-width' => 300 }
);
my $cdst = $svg->group( id => 'cds_texts', style => { fill => '#ccccff' } );
my $trnaa = $svg->group(
id => 'trna_a',
style =>
{ 'stroke' => '#3399ff', 'fill' => 'none', 'stroke-width' => 200 }
);
my $trnax = $svg->group(
id => 'trna_x',
style =>
{ 'stroke' => '#00ffcc', 'fill' => 'none', 'stroke-width' => 200 }
);
my $yaji = $svg->group(
id => 'yajirushi',
style =>
{ 'stroke' => '#ccffcc', 'fill' => 'none', 'stroke-width' => 5 }
);
my $rrnaa = $svg->group(
id => 'rrna_a',
style =>
{ 'stroke' => '#ff6699', 'fill' => 'none', 'stroke-width' => 200 }
);
my $rrnax = $svg->group(
id => 'rrna_x',
style =>
{ 'stroke' => '#ff9933', 'fill' => 'none', 'stroke-width' => 200 }
);
my $gcska = $svg->group(
id => 'gccontent',
style =>
{ 'stroke' => '#ff9933', 'fill' => 'none', 'stroke-width' => 3 }
);
my $gcskc = $svg->group(
id => 'gccontent_b',
style =>
{ 'stroke' => '#cc6611', 'fill' => 'none', 'stroke-width' => 3 }
);
my $gcskb = $svg->group(
id => 'gcskew',
style =>
{ 'stroke' => '#ccff66', 'fill' => 'none', 'stroke-width' => 3 }
);
my $gcskd = $svg->group(
id => 'gcskew_b',
style =>
{ 'stroke' => '#aadd44', 'fill' => 'none', 'stroke-width' => 3 }
);
my $oriter = $svg->group(
id => 'ori_ter',
style =>
{ 'stroke' => '#cccc33', 'fill' => 'none', 'stroke-width' => 20 }
);
my $title = $gb->{FEATURE0}->{organism};
my $text1 = $svg->text(
id => 'title',
'text-anchor' => 'middle',
x => $cx,
y => $cy,
fill => '#cccccc',
'font-size' => 200,
'font-family' => 'Gill Sans'
)->cdata($title);
my ( $xe, $ye ) = &get_pos( 0, 3700, $bp_length );
if(0){
my ( $xe2, $ye2 ) = &get_pos( 0, 2850, $bp_length );
$oriter->path( 'd' => "M$xe2,$ye2 L$xe,$ye" );
( $xe, $ye ) = &get_pos( 0, 2200, $bp_length );
( $xe2, $ye2 ) = &get_pos( 0, 1300, $bp_length );
$oriter->path( 'd' => "M$xe2,$ye2 L$xe,$ye" );
my ( $xe, $ye ) = &get_pos( length($gb->{SEQ}), 3700, $bp_length );
my ( $xe2, $ye2 ) = &get_pos( length($gb->{SEQ}), 2850, $bp_length );
$oriter->path( 'd' => "M$xe2,$ye2 L$xe,$ye" );
( $xe, $ye ) = &get_pos( length($gb->{SEQ}), 2200, $bp_length );
( $xe2, $ye2 ) = &get_pos( length($gb->{SEQ}), 1300, $bp_length );
$oriter->path( 'd' => "M$xe2,$ye2 L$xe,$ye" );
}
open( PWRITER, ">./data/" . $wfile . ".coord" );
if($gb->{LOCUS}->{circular} == 1){
( $xe, $ye ) = &get_pos( $ori, 4000, $bp_length );
$oriter->path( 'd' => "M$cx,$cy L$xe,$ye" );
if ( $xe < $cx ) {
$cdst->text(
'text-anchor' => 'end',
x => $xe,
y => $ye,
'font-size' => 100
)->cdata("ORIGIN");
}
else {
$cdst->text( x => $xe, y => $ye, 'font-size' => 100 )->cdata("ORIGIN");
}
($xe, $ye ) = &get_pos( $ter, 4000, $bp_length );
$oriter->path( 'd' => "M$cx,$cy L$xe,$ye" );
if ( $xe < $cx ) {
$cdst->text(
'text-anchor' => 'end',
x => $xe,
y => $ye,
'font-size' => 100
)->cdata("TERMINUS");
} else {
$cdst->text( x => $xe, y => $ye, 'font-size' => 100 )->cdata("TERMINUS");
}
}
my $num = $bp_length;
while ( $num =~ s/(.*\d)(\d\d\d)/$1,$2/ ) { }
my $text2 = $svg->text(
id => 'chromosome',
'text-anchor' => 'middle',
x => $cx,
y => $cy + 200,
fill => '#cccccc',
'font-size' => 150,
'font-family' => 'Gill Sans'
)->cdata( sprintf("%s: %s", $gb->id(), $optionalText) ) if(length($optionalText));
my $text2 = $svg->text(
id => 'bplength',
'text-anchor' => 'middle',
x => $cx,
y => $cy + 400,
fill => '#cccccc',
'font-size' => 150,
'font-family' => 'Gill Sans'
)->cdata( $num . " bp" );
my $i = 0;
$sclb->circle( cx => $cx, cy => $cy, r => 3750 );
$sclc->circle( cx => $cx, cy => $cy, r => 3680 );
while ( $i < $bp_length ) {
( $xe, $ye ) = &get_pos( $i, 3700, $bp_length );
$scla->path( 'd' => "M$cx,$cy L$xe,$ye" );
$cdst->text( x => $xe, y => $ye )->cdata( $i . "bp" );
( $xe, $ye ) = &get_pos( $i, 2850, $bp_length );
$cdst->text( x => $xe, y => $ye )->cdata( $i . "bp" );
( $xe, $ye ) = &get_pos( $i, 1800, $bp_length );
$cdst->text( x => $xe, y => $ye )->cdata( $i . "bp" );
if ( $i % 250000 == 0 ) {
my ( $xs, $ys ) = &get_pos( $i, 3630, $bp_length );
my ( $xe, $ye ) = &get_pos( $i, 3680, $bp_length );
$sclc->path( 'd' => "M$xs,$ys L$xe,$ye" );
$cdst->text(
'text-anchor' => 'middle',
x => $xe,
y => $ye,
'font-size' => 80
)->cdata( $i . "bp" );
}
$i = $i + 25000;
}
for ( $i = 0 ; $i < 100 ; $i++ ) {
my ( $xs, $ys ) = &get_posp( $i, 3700, $bp_length );
my ( $xe, $ye ) = &get_posp( $i, 3750, $bp_length );
$sclc->path( 'd' => "M$xs,$ys L$xe,$ye" );
if ( $i % 10 == 0 ) {
if ( $xe < $cx ) {
$cdst->text(
'text-anchor' => 'end',
x => $xe,
y => $ye,
'font-size' => 80
)->cdata( $i, "\%" );
} else {
$cdst->text( x => $xe, y => $ye, 'font-size' => 80 )->cdata( $i, "\%" );
}
}
}
for my $feature ( $gb->feature() ) {
my($xs, $ys, $xe, $ye);
my $strokeW = 300;
my $r = 3400;
if ( $gb->{$feature}->{type} eq "gene" and $gb->{$feature}->{direction} eq "direct" ) {
$r = 3400;
( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
if ($gb->{LOCUS}->{circular} == 0){
if($gb->{$feature}->{start}/(length($gb->{SEQ})) > 47/48){
my $startbp = $gb->{$feature}->{start} - int(length($gb->{SEQ}) * 47/48);
my $startpx = $startbp / int(length($gb->{SEQ}) * 1/48);
$strokeW = 300 - ($startpx * 300);
$r += int($strokeW/2) - 150;
( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
}
}
}elsif ( $gb->{$feature}->{type} eq "gene" and $gb->{$feature}->{direction} eq "complement" ){
$r = 3100;
( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
if ($gb->{LOCUS}->{circular} == 0){
if($gb->{$feature}->{start}/(length($gb->{SEQ})) > 47/48){
my $startbp = $gb->{$feature}->{start} - int(length($gb->{SEQ}) * 47/48);
my $startpx = $startbp / int(length($gb->{SEQ}) * 1/48);
$strokeW = 300 - ($startpx * 300);
$r -= int($strokeW/2) - 150;
( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
}
}
}
if($gb->{$feature}->{type} eq "gene"){
if ($gb->{LOCUS}->{circular} == 1){
if(query_strand($gb, $feature) eq 'leading'){
$count_a++;
if($count_a % 2 == 1 ) {
$cdsa->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width'=>$strokeW
);
}else{
$cdsb->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width'=>$strokeW
);
}
}else{
$count_b++;
if($count_a % 2 == 1 ) {
$cdsx->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width' => $strokeW
);
} else {
$cdsy->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width' => $strokeW
);
}
}
}else{
if($gb->{$feature}->{direction} eq 'direct'){
$count_a++;
if($count_a % 2 == 1 ) {
$cdsa->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width'=>$strokeW
);
}else{
$cdsb->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width'=>$strokeW
);
}
}else{
$count_b++;
if($count_a % 2 == 1 ) {
$cdsx->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width' => $strokeW
);
} else {
$cdsy->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye",
'stroke-width' => $strokeW
);
}
}
}
my ( $xm, $ym ) = &get_mapp( ( $xs + $xe ) / 2, ( $ys + $ye ) / 2, $bp_length );
my $feat = $gb->next_feature($feature);
printf PWRITER "%s\t%s\t%s\t%d\t%d\n", $feat, $gb->{$feat}->{type}, $gb->{$feat}->{gene}, $xm, $ym;
}
if ( $gb->{$feature}->{type} eq "tRNA" and $gb->{$feature}->{direction} eq "direct" ){
my $r = 2600;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
$trnaa->path( 'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye" );
my ( $xxs, $yys, $xxe, $yye, $xl, $yl, $xr, $yr ) = &get_arrow( $gb->{$feature}->{start}, $r + 50, $bp_length );
$yaji->path( 'd' => "M$xxs $yys L$xxe $yye" );
$yaji->path( 'd' => "M$xxe $yye L$xl $yl" );
$yaji->path( 'd' => "M$xxe $yye L$xr $yr" );
}
if ( $gb->{$feature}->{type} eq "tRNA" and $gb->{$feature}->{direction} eq "complement" ){
my $r = 2600;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
$trnax->path( 'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye" );
my ( $xxs, $yys, $xxe, $yye, $xl, $yl, $xr, $yr ) = &get_arrowc( $gb->{$feature}->{start}, $r - 50, $bp_length );
$yaji->path( 'd' => "M$xxs $yys L$xxe $yye" );
$yaji->path( 'd' => "M$xxs $yys L$xl $yl" );
$yaji->path( 'd' => "M$xxs $yys L$xr $yr" );
}
if ( $gb->{$feature}->{type} eq "rRNA" and $gb->{$feature}->{direction} eq "direct" ){
my $r = 2400;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
$rrnaa->path( 'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye" );
}
if ( $gb->{$feature}->{type} eq "rRNA" and $gb->{$feature}->{direction} eq "complement" ){
my $r = 2400;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
$rrnax->path( 'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye" );
}
}
if($gb->{LOCUS}->{circular} == 0){
my $ye1 = $cy - 3000;
my $ye2 = $cy - 3500;
$oriter->path( 'd' => "M$cx,$ye1 L$cx,$ye2", opacity=>0.5 );
my $r = 3550;
my ( $rx, $ry2 ) = &get_pos( int(length($gb->{SEQ}) * 47/48), $r, $bp_length );
$oriter->path( 'd' => "M$cx,$ry L$rx,$ry2", opacity=>0.2 );
my $r = 2950;
my ( $rx, $ry2 ) = &get_pos( int(length($gb->{SEQ}) * 47/48), $r, $bp_length );
$oriter->path( 'd' => "M$cx,$ry L$rx,$ry2", opacity=>0.2 );
}
my $bline = 2000;
my $blineg = 1500;
my ( $px, $py ) = &get_pos( 0, $bline, $bp_length );
my ( $pxg, $pyg ) = &get_pos( 0, $blineg, $bp_length );
my $pgcc = 0.5;
my $pgcs = 0.0;
my $range = 1000;
my $wsize = 2000;
my $step = 1000;
$tag = $svg->circle(
cx => $cx,
cy => $cy,
r => $bline,
stroke => '#33ff99',
fill => 'none'
);
$tag = $svg->circle(
cx => $cx,
cy => $cy,
r => $blineg,
stroke => '#66ffff',
fill => 'none'
);
for ( my $i = 0 ; $i + $wsize <= $bp_length ; $i += $step ) {
my $temp = substr( $gb->{SEQ}, $i, $wsize );
my $c_g = $temp =~ tr/g/g/;
my $c_c = $temp =~ tr/c/c/;
my $c_a = $temp =~ tr/a/a/;
my $c_t = $temp =~ tr/t/t/;
my $opacity = 1;
if($i > (length($gb->{SEQ}) * 95/96)){# || $i < length($gb->{SEQ}) * 1/96){
$opacity = 0.1 if($gb->{LOCUS}->{circular} == 0);
}
my $gc_content = 0;
$gc_content = ( $c_g + $c_c ) / ( $c_g + $c_c + $c_a + $c_t )
if ( $c_g + $c_c + $c_a + $c_t );
my ( $x, $y ) = &get_pos( $i, ( $bline + ( $gc_content - 0.5 ) * $range * 2 ), $bp_length );
if($pgcc >= 0.5 && $gc_content >= 0.5){
$gcska->path( 'd' => "M$px,$py L$x,$y", opacity=>$opacity );
}elsif($pgcc <= 0.5 && $gc_content <= 0.5){
$gcskc->path( 'd' => "M$px,$py L$x,$y", opacity=>$opacity );
}else{
my ( $xn, $yn ) = &get_pos( $i, $bline, $bp_length );
if($gc_content > 0.5){
$gcska->path( 'd' => "M$xn,$yn L$x,$y", opacity=>$opacity );
$gcskc->path( 'd' => "M$px,$py L$xn,$yn", opacity=>$opacity );
}else{
$gcska->path( 'd' => "M$px,$py L$xn,$yn", opacity=>$opacity );
$gcskc->path( 'd' => "M$xn,$yn L$x,$y", opacity=>$opacity );
}
}
my $gc_skew = 0;
$gc_skew = ( $c_c - $c_g ) / ( $c_g + $c_c ) if ( $c_g + $c_c );
my ( $xg, $yg ) = &get_pos( $i, ( $blineg + ($gc_skew) * $range * 2 ), $bp_length );
if($pgcs >= 0 && $gc_skew >= 0){
$gcskb->path( 'd' => "M$pxg,$pyg L$xg,$yg", opacity=>$opacity );
}elsif($pgcs <= 0 && $gc_skew <= 0){
$gcskd->path( 'd' => "M$pxg,$pyg L$xg,$yg", opacity=>$opacity );
}else{
my ( $xn, $yn ) = &get_pos( $i, $blineg, $bp_length );
if($gc_skew > 0){
$gcskb->path( 'd' => "M$xn,$yn L$xg,$yg", opacity=>$opacity );
$gcskd->path( 'd' => "M$pxg,$pyg L$xn,$yn", opacity=>$opacity );
}else{
$gcskb->path( 'd' => "M$pxg,$pyg L$xn,$yn", opacity=>$opacity );
$gcskd->path( 'd' => "M$xn,$yn L$xg,$yg", opacity=>$opacity );
}
}
$px = $x;
$py = $y;
$pxg = $xg;
$pyg = $yg;
$pgcc = $gc_content;
$pgcs = $gc_skew;
}
$cdst->text(
'text-anchor' => 'middle',
x => $cx,
y => 1750,
'font-size' => 120
)->cdata("GC-contents");
$cdst->text(
'text-anchor' => 'middle',
x => $cx,
y => 3000,
'font-size' => 120
)->cdata("GC-skew");
close PWRITER;
open( WRITER, ">./graph/" . $filename );
print WRITER $svg->xmlify;
close WRITER;
if($gmap){
generateGMap("graph/$filename");
}} | sub genome_map
{ &opt_default(output=>"show", name=>1, window=>50, amp=>1.5);
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $acnum = $gb->{LOCUS}->{id};
my $output = opt_val("output");
my $name = opt_val("name");
my $filename;
my $topmargin = 30;
my $sidemargin = 80;
my $hblock = 100;
my $vblock = 10;
my $page = 1;
my $start;
my $width = 800;
my $height = 600;
my $i = 0;
my $cds = 1;
my $window=opt_val("window");
my $amp = opt_val("amp");
mkdir ("graph", 0777);
for ($start = 1; $start <= length($gb->{SEQ}); $start += $window * 700 * 10){
my $end = $start + 10 * $window * 700 - 1;
my $im = new GD::Image($width, $height);
my $white = $im->colorAllocate(255,255,255);
my $black = $im->colorAllocate(0,0,0);
my $gray = $im->colorAllocate(180,180,180);
my $red = $im->colorAllocate(255,0,0);
my $yellow = $im->colorAllocate(255,255,0);
my $green = $im->colorAllocate(0,150,0);
my $blue = $im->colorAllocate(0,0,255);
my $aqua = $im->colorAllocate(120, 160, 255);
my $gred = $im->colorAllocate(255,150,150);
my $gyellow = $im->colorAllocate(255,255,50);
my $ggreen = $im->colorAllocate(150,150,150);
my $gblue = $im->colorAllocate(150,150,255);
for ($i = $sidemargin; $i <= $sidemargin + $hblock * 7; $i += $hblock){
$im->line($i, $topmargin, $i, $topmargin + 5 * 11 * $vblock,
$gray);
}
for ($i = $topmargin; $i <= $topmargin + $vblock * 5 * 11; $i +=
$vblock){
$im->line($sidemargin, $i, $sidemargin + 7 * $hblock, $i, $gray);
}
for ($i = $topmargin + $vblock * 5;
$i < $topmargin + $vblock * 5 * 11;
$i += $vblock * 5){
$im->line($sidemargin, $i - 1, $sidemargin + 7 * $hblock, $i - 1,
$black);
$im->line($sidemargin, $i + 1, $sidemargin + 7 * $hblock, $i + 1,
$black);
}
$im->string(gdSmallFont, $width - 110, 5,
"G-language Project", $black);
$im->string(gdSmallFont, $width - 110 - 50, 5, "A", $red);
$im->string(gdSmallFont, $width - 110 - 40, 5, "T", $green);
$im->string(gdSmallFont, $width - 110 - 30, 5, "G", $yellow);
$im->string(gdSmallFont, $width - 110 - 20, 5, "C", $blue);
my $j = 0;
for ($i = $topmargin + $vblock * 5;
$i <= $topmargin + $vblock * 5 * 10;
$i += $vblock * 5){
my $num = $start + $j * $window * 700;
$im->string(gdTinyFont, 10, $i, "$num", $black);
$j ++;
}
$im->string(gdSmallFont, 5, 5, "$acnum : from $start to $end",
$black);
my ($pa, $pt, $pg, $pc, $num, $color);
my $locus = 0;
for ($i = $start - 1; $i <= $start + 700 * 10 * $window - 1; $i += $window){
last if ($i + $window >= length($gb->{SEQ}));
my $seq = $gb->getseq($i, $i + $window - 1);
my $a = $seq =~ tr/a/a/;
my $t = $seq =~ tr/t/t/;
my $g = $seq =~ tr/g/g/;
my $c = $seq =~ tr/c/c/;
if ($a >= $t && $a >= $g && $a >= $c){
my $num = int($a / $window * 100);
$color = $red;
}elsif ($t >= $a && $t >= $g && $t >= $c){
my $num = int($t / $window * 100);
$color = $green;
}elsif ($g >= $a && $g >= $t && $g >= $c){
my $num = int($g / $window * 100);
$color = $yellow;
}elsif ($c >= $a && $c >= $t && $c >= $g){
my $num = int($c / $window * 100);
$color = $blue;
}
$im->setPixel($sidemargin + 1 + $locus % (700),
$topmargin + (int($locus / 700) + 1) * $vblock * 5,
$color);
my $dist = 7;
if ($locus % $dist == $dist - 1){
$num = int($a / int ($window * $amp) * 100) + 5;
$im->line($sidemargin - $dist + $locus % (700), $pa,
$sidemargin + $locus % (700),
$topmargin - $num
+ (int($locus / 700) + 1) * $vblock * 5,
$gred);
$pa = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($t / int ($window * $amp) * 100) + 5;
$im->line($sidemargin - $dist + $locus % (700), $pt,
$sidemargin + $locus % (700),
$topmargin - $num
+ (int($locus / 700) + 1) * $vblock * 5,
$ggreen);
$pt = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($g / int ($window * $amp) * 100) + 5;
$im->line($sidemargin - $dist + $locus % (700), $pg,
$sidemargin + $locus % (700),
$topmargin - $num
+ (int($locus / 700) + 1) * $vblock * 5,
$gyellow);
$pg = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($c / int ($window * $amp) * 100) + 5;
$im->line($sidemargin - $dist + $locus % (700), $pc,
$sidemargin + $locus % (700),
$topmargin - $num
+ (int($locus / 700) + 1) * $vblock * 5,
$gblue);
$pc = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
}elsif($locus % 700 == 0){
$num = int($a / int ($window * $amp) * 100) + 5;
$pa = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($t / int ($window * $amp) * 100) + 5;
$pt = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($g / int ($window * $amp) * 100) + 5;
$pg = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
$num = int($c / int ($window * $amp) * 100) + 5;
$pc = $topmargin - $num +(int($locus / 700) + 1)
* $vblock * 5;
}
$locus ++;
}
my $flag = 0;
my $before = -5000;
my $before2 = -10000;
while (%{$gb->{"CDS$cds"}}){
my $cdsstart = $gb->{"CDS$cds"}->{start};
my $cdsend = $gb->{"CDS$cds"}->{end};
my $cdsdir = $gb->{"CDS$cds"}->{direction};
my $cdsdiff = $cdsstart - $before;
my $cdsdiff2 = $cdsstart - $before2;
if ($flag == 0){
if (int($cdsdiff / $window) < 20){
$flag = 1;
}
}elsif ($flag == 1){
if (int($cdsdiff / $window) < 20){
if (int($cdsdiff2 / $window) < 20){
$flag = 2;
}else{
$flag = 0;
}
}else{
$flag = 0;
}
}elsif ($flag == 2){
if (int($cdsdiff2 / $window) < 20){
$flag = 1;
}else{
$flag = 0;} | sub genome_map2
{ require SVG;
&opt_default(output=>"show", window=>50, type=>"CDS",
start=>1, end=>100000, filename=>"genome_map.svg", ptt=>'', cgi=>0);
my @args = opt_get(@_);
my $gb = shift @args;
my $acnum = $gb->{LOCUS}->{id};
my $output = opt_val("output");
my $filename = opt_val("filename");
my $topmargin = 60;
my $sidemargin = 80;
my $hblock = 100;
my $vblock = 10;
my $page = 1;
my $i = 0;
my $cds = 1;
my $window=opt_val("window");
my $start = opt_val("start");
my $end = opt_val("end");
my $ptt = opt_val("ptt");
my $cgi = opt_val("cgi");
my @type = split(/ /, opt_val("type"));
my $j2 = 0;
my $width = (int(($end - $start) / $hblock / $window) + 1) * $hblock + $sidemargin * 2;
my $height = $hblock/2 + $topmargin * 2 + scalar(@type) * $hblock - $vblock;
eval{
$ptt = set_gpac($gb, -ptt=>$ptt);
};
unless ($cgi){
sdb_save(\$ptt, "ptt");
sdb_save($gb, "gb");
}
my $svg = SVG->new(width=>$width, height=>$height);
for ($i = $sidemargin; $i <= $width - $sidemargin; $i += $hblock){
$svg->line(id=>"bvline$i", x1=>$i,
y1=>$topmargin, x2=>$i, y2=>($hblock * (scalar(@type) + 1) + $vblock),
style=>{
stroke=>"darkgray", 'stroke-width'=>1,
'stroke-opacity'=>0.2
});
}
for ($i = $sidemargin; $i < $width - $sidemargin; $i += $hblock){
$svg->text(
id=>"num$i",
x=>$i, y=>($topmargin - 5), fill=>"black",
'font-size'=>8,
)->cdata(((($i - $sidemargin) + 1) * $window - 49 + $start - 1) . " bp");
}
for ($i = $topmargin; $i <= $topmargin + $vblock * 5 ; $i += $vblock){
$svg->line(id=>"bhline$i", x1=>$sidemargin,
y1=>$i, x2=>($width - $sidemargin), y2=>$i,
style=>{
stroke=>"darkgray", 'stroke-width'=>1,
'stroke-opacity'=>0.2
});
}
for ($i = $topmargin + $vblock * 5;
$i <= $topmargin + $hblock * (scalar(@type) + 1); $i += $hblock){
$svg->line(id=>"bhlline$i", x1=>$sidemargin,
y1=>$i, x2=>($width - $sidemargin), y2=>$i,
style=>{
stroke=>"darkgray", 'stroke-width'=>1,
'stroke-opacity'=>0.2
});
}
for ($i = $topmargin + $vblock * 5 + $hblock / 2;
$i <= $topmargin + $hblock * scalar(@type); $i += $hblock){
$svg->line(id=>"dnau$i", x1=>$sidemargin,
y1=>($i - 1), x2=>($width - $sidemargin), y2=>($i - 1),
style=>{
stroke=>"black", 'stroke-width'=>1,
'stroke-opacity'=>1
});
$svg->line(id=>"dnad$i", x1=>$sidemargin,
y1=>($i + 1), x2=>($width - $sidemargin), y2=>($i + 1),
style=>{
stroke=>"black", 'stroke-width'=>1,
'stroke-opacity'=>1
});
}
$svg->text(
id=>"A",
x=>20, y=>($topmargin + $vblock * 3), fill=>"red",
'font-size'=>10,
)->cdata("A");
$svg->text(
id=>"T",
x=>30, y=>($topmargin + $vblock * 3), fill=>"green",
'font-size'=>10,
)->cdata("T");
$svg->text(
id=>"G",
x=>40, y=>($topmargin + $vblock * 3), fill=>"gold",
'font-size'=>10,
)->cdata("G");
$svg->text(
id=>"C",
x=>50, y=>($topmargin + $vblock * 3), fill=>"blue",
'font-size'=>10,
)->cdata("C");
my ($pa, $pt, $pg, $pc, $num, $color);
my (@gra, @grt, @grc, @grg);
my $locus = 0;
for ($i = $start - 1; $i <= $end; $i += $window){
my $seq = $gb->getseq($i, $i + $window * 2 - 1);
my $a = $seq =~ tr/a/a/;
my $t = $seq =~ tr/t/t/;
my $g = $seq =~ tr/g/g/;
my $c = $seq =~ tr/c/c/;
my $x = $seq =~ tr/x/x/;
my $n = $seq =~ tr/n/n/;
if ($locus % 2 != 1){
if ($a >= $t && $a >= $g && $a >= $c){
my $num = int($a / $window * 100);
$color = 'red';
$color = 'white' if ($a == 0);
}elsif ($t >= $a && $t >= $g && $t >= $c){
my $num = int($t / $window * 100);
$color = 'green';
}elsif ($g >= $a && $g >= $t && $g >= $c){
my $num = int($g / $window * 100);
$color = 'yellow';
}elsif ($c >= $a && $c >= $t && $c >= $g){
my $num = int($c / $window * 100);
$color = 'blue';
}
my $j;
for ($j = $topmargin + $vblock * 5 + $hblock / 2;
$j <= $topmargin + $hblock * scalar(@type);
$j += $hblock
){
last if ($locus >= int($width - $sidemargin * 2) - 3);
$j2 ++;
$svg->line(id=>"dnac$j-$j2", x1=>($sidemargin + 1 + $locus),
y1=>$j, x2=>($sidemargin + 3 + $locus), y2=>$j,
style=>{
stroke=>$color, 'stroke-width'=>1,
'stroke-opacity'=>1
});
}
}
my $dist = 5;
if ($locus % $dist == $dist -1 || $locus == 0){
last if ($a == 0 && $t == 0 && $c == 0 && $g == 0 && $x == 0 && $n == 0);
push (@gra, sprintf("%d,%d", $sidemargin + $locus,
$topmargin + $vblock * 5 - int($a / 2 / $window * 100 ) + 5));
push (@grt, sprintf("%d,%d", $sidemargin + $locus,
$topmargin + $vblock * 5 - int($t / 2 / $window * 100 ) + 5));
push (@grg, sprintf("%d,%d", $sidemargin + $locus,
$topmargin + $vblock * 5 - int($g / 2 / $window * 100 ) + 5));
push (@grc, sprintf("%d,%d", $sidemargin + $locus,
$topmargin + $vblock * 5 - int($c / 2 / $window * 100 ) + 5));
}
$locus ++;
}
$svg->polyline(id=>"gra", points=>join(" ", @gra),
style=>{
stroke=>'red', 'stroke-width'=>1,
'stroke-opacity'=>0.2, fill=>'none'
});
$svg->polyline(id=>"grt", points=>join(" ", @grt),
style=>{
stroke=>'green', 'stroke-width'=>1,
'stroke-opacity'=>0.2, fill=>'none'
});
$svg->polyline(id=>"grg", points=>join(" ", @grg),
style=>{
stroke=>'yellow', 'stroke-width'=>1,
'stroke-opacity'=>0.2, fill=>'none'
});
$svg->polyline(id=>"grc", points=>join(" ", @grc),
style=>{
stroke=>'blue', 'stroke-width'=>1,
'stroke-opacity'=>0.2, fill=>'none'
});
my $flag = 0;
my $before = -5000;
my $before2 = -10000;
my @colors = qw(J K L D O M N P T C G E F H I Q R S -);
my $col = 0;
foreach my $pat (@type){
$svg->text(
id=>$pat,
x=>20, y=>($topmargin + $vblock * 5 + $hblock * $col + $hblock/2 + 3),
'font-size'=>10,
)->cdata($pat);
foreach my $cds ($gb->feature()){
next unless($gb->{$cds}->{end} >= $start && $gb->{$cds}->{start} <= $end);
next unless($gb->{$cds}->{type} eq $pat);
my $cdsstart = $gb->{$cds}->{start};
my $cdsend = $gb->{$cds}->{end};
my $cdsdir = $gb->{$cds}->{direction};
my $cdsdiff = $cdsstart - $before;
my $genename = $gb->{$cds}->{gene};
my $code = $gb->{$cds}->{code} || $colors[$col];
my $dif1 = -10;
my $sign = -1;
$dif1 = -25 if ($cdsdiff / $window < 15);
if ($cdsdir eq 'complement'){
$dif1 *= -1;
$sign *= -1;
}
$cdsstart = $start if ($cdsstart < $start);
$cdsend = $end if ($cdsend > $end);
if ($cdsdir eq 'direct'){
$svg->rect(
id=>"liner$cds", x=>($sidemargin + ($cdsstart - $start)/$window),
y=>($topmargin + $dif1 + $vblock * 5 + $hblock / 2 - 3 + $hblock * $col),
height=>(abs($dif1) + 3),
width=>(($cdsend - $cdsstart)/$window),
style=>{
stroke=>"gray", 'stroke-width'=>1,
'stroke-opacity'=>0.2, 'fill'=>'none'
});
}else{
$svg->rect(
id=>"liner2$cds", x=>($sidemargin + ($cdsstart - $start)/$window),
y=>($topmargin + $vblock * 5 + $hblock / 2 - 1 + $hblock * $col),
height=>(abs($dif1) + 3),
width=>(($cdsend - $cdsstart)/$window),
style=>{
stroke=>"gray", 'stroke-width'=>1,
'stroke-opacity'=>0.2, 'fill'=>'none'
});
}
$svg->anchor(
-href=>'http://localhost/g-language/genome_view.cgi?pos=' . $cds,
-target=>'_blank'
)->rect(
id=>"line$cds", x=>($sidemargin + ($cdsstart - $start)/$window),
y=>($topmargin + $dif1 + $vblock * 5 + $hblock / 2 - 3 + $hblock * $col),
height=>5,
width=>(($cdsend - $cdsstart)/$window),
style=>{
stroke=>"green", 'stroke-width'=>1,
'stroke-opacity'=>0.2, 'fill'=>$COG_fcolor{$code},
'fill-opacity'=>0.2
});
$svg->text(
id=>"cds$cds",
x=>($sidemargin + ($cdsstart - $start)/$window),
y=>($topmargin + (abs($dif1) + 6) * $sign + $vblock * 5 + $hblock / 2 + 1 + $hblock * $col),
fill=>$COG_fcolor{$code},
'font-size'=>5,
)->cdata($genename);
$before = $cdsstart;
}
$col ++;
}
my $topline = $svg->line(id=>"top", x1=>0, y1=>10, x2=>$width, y2=>10,
style=>{
stroke=>"plum", 'stroke-width'=>3,
'stroke-opacity'=>0.3
});
$topline->animate(
attributeName=>"stroke",
values=>join(';', values(%COG_fcolor)), dur=>"90s",
repeatDur=>'indefinite'
);
my $bottomline = $svg->line(id=>"bottom", x1=>0, y1=>($height-10), x2=>$width, y2=>($height-10),
style=>{
stroke=>"plum", 'stroke-width'=>3,
'stroke-opacity'=>0.3
});
$bottomline->animate(
attributeName=>"stroke",
values=>join(';', values(%COG_fcolor)), dur=>"90s",
repeatDur=>'indefinite'
);
$svg->anchor(
-href=>"http://www.g-language.org/",
-target=>"_blank"
)->text(
id=>"credits",
x=>($width - 300), y=>($height - 15), fill=>"darkgray",
'font-size'=>8, 'font-style'=>'italic',
)->cdata(
"generated by genome_map2, G-language Genome Analysis Environment"
);
$svg->text(
id=>"locus1",
x=>30, y=>26, fill=>"navy",
'font-size'=>10,
)->cdata("Accession Number: ", $gb->{LOCUS}->{id});
$svg->text(
id=>"locus2",
x=>250, y=>26, fill=>"navy",
'font-size'=>10,
)->cdata("Organism: ", $gb->{FEATURE0}->{organism});
$svg->text(
id=>"locus3",
x=>500, y=>26, fill=>"navy",
'font-size'=>10,
)->cdata(length($gb->{SEQ}) . " bp");
my $leftarrow = $svg->anchor(
-href=>'http://localhost/g-language/genome_view.cgi?pos=' . ($start - 50000)
)->polygon(
id=>"larrow",
points=>sprintf("%d,%d %d,%d %d,%d", 50,
$topmargin + $vblock * 5 + $hblock * scalar(@type) - 10,
50,
$topmargin + $vblock * 5 + $hblock * scalar(@type) + 20,
15,
$topmargin + $vblock * 5 + $hblock * scalar(@type) + 5
),
style=>{
fill=>"plum", stroke=>"plum", 'stroke-width'=>5,
'fill-opacity'=>0.1, 'stroke-opacity'=>0.3
}
);
$leftarrow->animate(
attributeName=>"stroke",
values=>join(';', reverse(values(%COG_fcolor))), dur=>"90s",
repeatDur=>'indefinite'
);
$leftarrow->animate(
attributeName=>"fill",
values=>join(';', reverse(values(%COG_fcolor))), dur=>"90s",
repeatDur=>'indefinite'
);
my $rightarrow = $svg->anchor(
-href=>'http://localhost/g-language/genome_view.cgi?pos=' . ($end + 50001)
)->polygon(
id=>"rarrow",
points=>sprintf("%d,%d %d,%d %d,%d", $width - 50,
$topmargin + $vblock * 5 + $hblock * scalar(@type) - 10,
$width - 50,
$topmargin + $vblock * 5 + $hblock * scalar(@type) + 20,
$width - 15,
$topmargin + $vblock * 5 + $hblock * scalar(@type) + 5
),
style=>{
fill=>"plum", stroke=>"plum", 'stroke-width'=>5,
'fill-opacity'=>0.1, 'stroke-opacity'=>0.3
}
);
$rightarrow->animate(
attributeName=>"stroke",
values=>join(';', reverse(values(%COG_fcolor))), dur=>"90s",
repeatDur=>'indefinite'
);
$rightarrow->animate(
attributeName=>"fill",
values=>join(';', reverse(values(%COG_fcolor))), dur=>"90s",
repeatDur=>'indefinite'
);
mkdir ("graph", 0777);
open(OUT, '>graph/' . $filename) || msg_error($!);
print OUT $svg->xmlify;
close(OUT);
msg_gimv('graph/' . $filename) if ($output eq 'show');
return 1;} | sub genome_map3
{ &opt_default(output=>"show", width=>8192, height=>8192, datafilename=>'', gmap=>1, filename=>"genome_map3.png");
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $acnum = $gb->{LOCUS}->{id};
my $datafilename = opt_val("datafilename") || $gb->id() . '.coord';
my $output = opt_val("output");
my $filename = opt_val("filename");
my $topmargin = 50;
my $sidemargin = 150;
my $hblock = 100;
my $vblock = 10;
my $width = opt_val("width");
my $height = opt_val("height");
my $gmap = opt_val("gmap");
my $numHBlock = int(($width - $sidemargin - 50) / $hblock);
my $numVBlock = int(($height - $topmargin - 50) / ($vblock * 5));
my $window = int(length($gb->{SEQ}) / ($numHBlock * $numVBlock * $hblock)) + 1;
msg_error("Image size: $width x $height pixels.\nUsing Window size = $window bp to fit the whole genome...\n\n");
msg_error("Map generation will take a few minutes. Please make yourself comfortable until the image is generated ;-\)\n\n") if ($gmap);
my $start = 1;
my $end = length $gb->{SEQ};
my $i = 0;
my $cds = 1;
mkdir ("graph", 0777);
mkdir ("data", 0777);
open(OUT, '>' . 'data/' . $datafilename) || die($!);
my $im = new GD::Image($width, $height);
my $white = $im->colorAllocate(255,255,255);
my $black = $im->colorAllocate(0,0,0);
my $gray = $im->colorAllocate(180,180,180);
my $red = $im->colorAllocate(255,0,0);
my $yellow = $im->colorAllocate(255,255,0);
my $green = $im->colorAllocate(0,150,0);
my $blue = $im->colorAllocate(0,0,255);
my $aqua = $im->colorAllocate(120, 160, 255);
my $rrna = $im->colorAllocate(255, 160, 160);
my $trna = $im->colorAllocate(160, 255, 160);
my $gred = $im->colorAllocate(255,200,200);
my $gyellow = $im->colorAllocate(255,255,100);
my $ggreen = $im->colorAllocate(180,220,180);
my $gblue = $im->colorAllocate(200,200,255);
for ($i = $sidemargin; $i <= $sidemargin + $hblock * $numHBlock; $i += $hblock){
$im->line($i, $topmargin, $i, $topmargin + 5 * ($numVBlock + 1) * $vblock, $gray);
}
for ($i = $topmargin; $i <= $topmargin + $vblock * 5 * ($numVBlock + 1); $i += $vblock){
$im->line($sidemargin, $i, $sidemargin + $numHBlock * $hblock, $i, $gray);
}
for ($i = $topmargin + $vblock * 5; $i < $topmargin + $vblock * 5 * ($numVBlock + 1); $i += $vblock * 5){
$im->line($sidemargin, $i - 1, $sidemargin + $numHBlock * $hblock, $i - 1, $black);
$im->line($sidemargin, $i + 1, $sidemargin + $numHBlock * $hblock, $i + 1, $black);
}
$im->string(gdGiantFont, $width - 210, 5, "G-language Project", $black);
$im->string(gdGiantFont, $width - 210 - 50, 5, "A", $red);
$im->string(gdGiantFont, $width - 210 - 40, 5, "T", $green);
$im->string(gdGiantFont, $width - 210 - 30, 5, "G", $yellow);
$im->string(gdGiantFont, $width - 210 - 20, 5, "C", $blue);
my $j = 0;
for ($i = $topmargin + $vblock * 5; $i <= $topmargin + $vblock * 5 * $numVBlock; $i += $vblock * 5){
my $num = $start + $j * $window * $numHBlock * $numVBlock * $hblock;
$im->string(gdLargeFont, 10, $i, "$num", $black);
$j ++;
}
$im->string(gdGiantFont, 50, 5, "$acnum : from $start to $end", $black);
my ($pa, $pt, $pg, $pc, $num, $color);
my $locus = 0;
for ($i = $start - 1; $i + $window <= $end; $i += $window){
my $seq = $gb->getseq($i, $i + $window - 1);
my $a = $seq =~ tr/a/a/;
my $t = $seq =~ tr/t/t/;
my $g = $seq =~ tr/g/g/;
my $c = $seq =~ tr/c/c/;
if ($a >= $t && $a >= $g && $a >= $c){
my $num = int($a / $window * 100);
$color = $red;
}elsif ($t >= $a && $t >= $g && $t >= $c){
my $num = int($t / $window * 100);
$color = $green;
}elsif ($g >= $a && $g >= $t && $g >= $c){
my $num = int($g / $window * 100);
$color = $yellow;
}elsif ($c >= $a && $c >= $t && $c >= $g){
my $num = int($c / $window * 100);
$color = $blue;
}
$im->setPixel($sidemargin + 1 + $locus % (($hblock * $numHBlock)), $topmargin + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5, $color);
my $dist = 7;
if (($locus % (($hblock * $numHBlock))) % $dist == $dist - 1){
$num = int(($a / $window) * $vblock * 3.8) + 2;
$im->line($sidemargin - $dist + 1 + $locus % (($hblock * $numHBlock)), $pa,
$sidemargin + $locus % (($hblock * $numHBlock)),
$topmargin - $num + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5, $gred);
$pa = $topmargin - $num + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($t / $window) * $vblock * 3.8) + 2;
$im->line($sidemargin - $dist + 1 + $locus % (($hblock * $numHBlock)), $pt,
$sidemargin + $locus % (($hblock * $numHBlock)),
$topmargin - $num + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5, $ggreen);
$pt = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($g / $window) * $vblock * 3.8) + 2;
$im->line($sidemargin - $dist + 1 + $locus % (($hblock * $numHBlock)),
$pg, $sidemargin + $locus % (($hblock * $numHBlock)),
$topmargin - $num + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5, $gyellow);
$pg = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($c / $window) * $vblock * 3.8) + 2;
$im->line($sidemargin - $dist + 1 + $locus % (($hblock * $numHBlock)),
$pc, $sidemargin + $locus % (($hblock * $numHBlock)),
$topmargin - $num + (int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5, $gblue);
$pc = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
}elsif($locus % ($hblock * $numHBlock) == 0){
$num = int(($a / $window) * $vblock * 3.8) + 2;
$pa = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($t / $window) * $vblock * 3.8) + 2;
$pt = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($g / $window) * $vblock * 3.8) + 2;
$pg = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
$num = int(($c / $window) * $vblock * 3.8) + 2;
$pc = $topmargin - $num +(int($locus / ($hblock * $numHBlock)) + 1) * $vblock * 5;
}
$locus ++;
}
my $flag = 0;
my $before = -5000;
my $before2 = -10000;
foreach my $feat ($gb->feature()){
next unless($gb->{$feat}->{type} eq 'CDS' || $gb->{$feat}->{type} eq 'rRNA' || $gb->{$feat}->{type} eq 'tRNA');
my $cdsstart = $gb->{$feat}->{start};
my $cdsend = $gb->{$feat}->{end};
my $cdsdir = $gb->{$feat}->{direction};
my $cdsdiff = $cdsstart - $before;
my $cdsdiff2 = $cdsstart - $before2;
my $genename = $gb->{$feat}->{gene};
if ($flag == 0){
if (int($cdsdiff / $window) < 25){
$flag = 1;
}
}elsif ($flag == 1){
if (int($cdsdiff / $window) < 25){
if (int($cdsdiff2 / $window) < 25){
$flag = 2;
}else{
$flag = 0;
}
$flag = 0;
}else{
$flag = 0;} | sub plasmid_map
{ require SVG;
opt_default(ptt=>'', output=>'show', filename=>"plasmid_map.svg", cgi=>0);
my @args = opt_get(@_);
my $gb = shift;
my $ptt = opt_val("ptt");
my $output = opt_val("output");
my $filename = opt_val("filename");
my $cgi = opt_val("cgi");
eval{
$ptt = set_gpac($gb, -ptt=>$ptt);
};
unless ($cgi){
sdb_save(\$ptt, "ptt");
sdb_save($gb, "gb");
}
my $svg = SVG->new(width=>640, height=>400);
my $pi = atan2(1,1) * 4;
my $seqlen = length $gb->{SEQ};
my $maxlen;
foreach my $cds ($gb->cds()){
my $tmplen = length ($gb->get_geneseq($cds));
$maxlen = $tmplen if ($tmplen > $maxlen);
}
foreach my $cds ($gb->cds()){
my $id = $cds;
my $gene = $gb->get_geneseq($cds);
my $length = length $gene;
my $gc = int(log($maxlen) / log($length) * 30);
my $rad = 2 * $pi * $gb->{$cds}->{start} / $seqlen * -1 + $pi;
my ($x1, $x2, $y1, $y2);
if ($gb->{$cds}->{direction} eq 'direct'){
$x1 = (100 + 5) * sin($rad) + 200;
$y1 = (100 + 5) * cos($rad) + 200;
$x2 = (100 + $gc) * sin($rad) + 200;
$y2 = (100 + $gc) * cos($rad) + 200;
}else{
$x1 = (100 - $gc) * sin($rad) + 200;
$y1 = (100 - $gc) * cos($rad) + 200;
$x2 = (100 - 5) * sin($rad) + 200;
$y2 = (100 - 5) * cos($rad) + 200;
}
my $stroke = $COG_fcolor{$gb->{$cds}->{code}};
my $cdsstart = $gb->{$cds}->{start};
$svg->anchor(
-href=>'http://localhost/g-language/genome_view.cgi?pos=' . $cdsstart,
-target=>"_blank"
)->line(
id=>$id, x1=>$x1,
y1=>$y1, x2=>$x2, y2=>$y2,
style=>{
stroke=>$stroke, 'stroke-width'=>1,
'stroke-opacity'=>0.3
});
}
$svg->circle(id=>'genome', cx=>200, cy=>200, r=>100,
style=>{
stroke=>'blue', fill=>'none', 'stroke-width'=>5,
'stroke-opacity'=>0.2
});
my $x = 400;
my $y = 123;
my $y2 = 130;
$svg->anchor(
-href=>"http://www.ncbi.nih.gov/cgi-bin/COG/palox?fun=all",
-target=>"_blank"
)->text(
id=>"COG link",
x=>($x - 20), y=>($y2 - 30),
'font-size'=>9
)->cdata(
"Gene Classification based on NCBI COG functional categories"
);
foreach my $category (qw(J K L D O M N P T C G E F H I Q R S -)){
$svg->rect(id=>$category, x=>$x, y=>$y, width=>9, height=>8,
style=>{
stroke=>'none', fill=>$COG_fcolor{$category},
opacity=>0.3
});
my $id = $category . '_text';
$svg->text(id=>$id, x=>($x + 15), y=>$y2, 'font-size'=>7)->cdata($COG_fcode{$category});
$y += 12;
$y2 += 12;
}
my $topline = $svg->line(id=>"top", x1=>0, y1=>10, x2=>640, y2=>10,
style=>{
stroke=>"blue", 'stroke-width'=>3,
'stroke-opacity'=>0.3
});
$topline->animate(
attributeName=>"stroke",
values=>join(';', values(%COG_fcolor)), dur=>"90s",
repeatDur=>'indefinite'
);
my $bottomline = $svg->line(id=>"bottom", x1=>0, y1=>390, x2=>640, y2=>390,
style=>{
stroke=>"blue", 'stroke-width'=>3,
'stroke-opacity'=>0.3
});
$bottomline->animate(
attributeName=>"stroke",
values=>join(';', values(%COG_fcolor)), dur=>"90s",
repeatDur=>'indefinite'
);
$svg->anchor(
-href=>"http://www.g-language.org/",
-target=>"_blank"
)->text(
id=>"credits",
x=>380, y=>385, fill=>"darkgray",
'font-size'=>8, 'font-style'=>'italic',
)->cdata(
"generated by plasmid map, G-language Genome Analysis Environment"
);
$svg->text(
id=>"locus1",
x=>30, y=>30, fill=>"navy",
'font-size'=>10,
)->cdata("Accession Number: ", $gb->{LOCUS}->{id});
$svg->text(
id=>"locus2",
x=>250, y=>30, fill=>"navy",
'font-size'=>10,
)->cdata("Organism: ", $gb->{FEATURE0}->{organism});
$svg->text(
id=>"locus3",
x=>500, y=>30, fill=>"navy",
'font-size'=>10,
)->cdata("$seqlen bp");
mkdir('graph', 0777);
open(OUT, '>graph/' . $filename) || msg_error($!);
print OUT $svg->xmlify;
close(OUT);
msg_gimv('graph/' . $filename) if ($output eq "show");
return 1;} |