G::Seq
GenomeMap
Summary
G::Seq::GenomeMap - Collection of methods for creating genome maps.
Package variables
Privates (from "my" definitions)
$gene = $gb->{$cds}->{gene} or $gb->{$cds}->{locus_tag}
$cy = 4000
%COG_fcolor = ( J=>"plum", K=>"fuchsia", L=>"pink", D=>"lightgreen", O=>"green", M=>"khaki", N=>"greenyellow", P=>"darkkhaki", T=>"cyan", C=>"blue", G=>"mediumturquoise", E=>"lightskyblue", F=>"mediumpurple", H=>"aqua", I=>"blueviolet", Q=>"lightskyblue", R=>"gainsboro", S=>"darkgrey", '-'=>"aliceblue" )
$k;(1)
$l(1) = int ($k / $window)
$dif1(2) = -3
$dif2(1) = -2 - 3
$k;(2)
$dif2(3) = -7 - 2
$dif2(2) = -2 - 3
$blockcolor = $aqua
$genename = $gb->{"FEATURE$feat"}->{gene}
$l(2) = int ($k / $window)
$dif1(1) = -3
%COG_fcode = ( J=>"Translation, ribosomal structure and biogenesis", K=>"Transcription", L=>"DNA replication, recombination and repair", D=>"Cell division and chromosome partitioning", O=>"Posttranslational modification, protein turnover, chaperones", M=>"Cell envelope biogenesis, outer membrane", N=>"Cell motility and secretion", P=>"Inorganic ion transport and metabolism", T=>"Signal transduction mechanisms", C=>"Energy production and conservation", G=>"Carbohydrate transport and metabolism", E=>"Amino acid transport and metabolism", F=>"Nucleotide transport and metabolism", H=>"Coenzyme metabolism", I=>"Lipid metabolism", Q=>"Secondary metabolites biosynthesis, transport and catabolism", R=>"General function prediction only", S=>"Function unknown", '-'=>"Non COG" )
$dif1(3) = -2
$feat = $gb->{"CDS$cds"}->{feature}
$dif3(2) = -2 - 15 - 9 + (-12 * $flag)
$k;(3)
$dif3(1) = -2 - 4 - 9 + (-9 * $flag)
$pi = 4 * atan2(1,1)
$cx = 4000
$l(3) = int ($k / $window)
$type = $gb->{$cds}->{type}
Included modules
Inherit
Exporter
Synopsis
No synopsis!
Description
This class is a part of G-language Genome Analysis Environment,
collecting methods for creating genome maps.
Methods
Methods description
Name: circular_map - draws circular map of the genome
Description:
This method creates a circular map of the genome using SVG,
suitable for plasmids and circular bacterial chromosomes.
From the outer ring inwards, genes on direct strand (pink),
genes on complementary strand (yellow), tRNAs (green arrows),
rRNAs (pink or orange stripes depending on the strand),
GC content (brown lines), GC skew (yellow lines). Replication
origin and terminus predicted from the GC skew shift points
are also labeled.
Generated SVG is very large (8000x8000 pixels), and it is
suited to be converted to Google Map View with generate_gmap().
Output file is created in the "graph" directory, with
the accession number as file name and ".svg" as extension.
Usage:
NULL = circular_map($gb);
Options:
-gmap 1 to create Google Map view, 0 to only generate PNG image
(default:1)
Author:
Nobuhiro Kido (t07505nk@sfc.keio.ac.jp)
History:
20080414-01 added gmap option
20071023-01 initial posting |
Name: dnawalk - draws DNA Walk map of the genome
Description:
This method draws the DNA Walk map of the given genome.
DNA Walk is drawn by moving a single pixel per nucleotide,
in the direction specified for each base. Here A is moved
upward, T downward, G to the right, and C to the left.
Position zero (first letter of the genome) is indicated
by the crossing of thin axes.
Generated PNG is very large (8000x8000 pixels), and it is
suited to be converted to Google Map View with generate_gmap().
Output file is created in the "graph" directory, with
the accession number as file name and ".png" as extension.
Usage:
NULL = dnawalk($gb);
Options:
-gmap 1 to create Google Map view, 0 to only generate PNG image
(default:1)
Author:
Keita Ikegami (t06056ki@sfc.keio.ac.jp)
History:
20080414-01 added gmap option
20071023-01 initial posting |
Name: genome_map - draws the map of the genome
Description:
This method creates a map of the genome, showing the local
nucleotide contents and positions of genes.
A is shown in red, T is shown in green,
G is shown in yellow, and C is shown in blue.
This method generates the entire genome map using
multiple 800x600 pixel image in PNG (via GD library).
Usage:
NULL = genome_map($gb);
Options:
-name print gene name (default: 1)
-window number of nucleotides represented by one pixel (default: 50)
-amp height of the nucleotide content graph (default: 1.5)
-output "g" for graph, "show" for display (default: "show")
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20010906-01 initial posting |
Name: genome_map2 - draws the map of the genome (version 2)
Description:
This method creates a map of the genome, showing the local
nucleotide contents and positions of genes using SVG.
A is shown in red, T is shown in green,
G is shown in yellow, and C is shown in blue.
Map of the specified position (with -start and -end options)
is generated in SVG format.
Usage:
NULL = genome_map2($gb);
Options:
-window length of one pixel (default: 50)
-type type of features to print (default: CDS)
-output "g" for graph, "show" for display (default: "show")
-start start position (default: 1)
-end end position (default: 100000)
-filename output file name (default: genome_map.svg)
-ptt ptt filename
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20020906-01 initial posting |
Name: genome_map3 - draws the map of the genome (version 3)
Description:
This method creates a map of the genome, showing the local
nucleotide contents and positions of genes.
A is shown in red, T is shown in green,
G is shown in yellow, and C is shown in blue.
Entire genome is prepresented in a very large PNG image
(8192x8192 pixel by default), and the number of nucleotides
represented by one pixel is automatically calculated. Then
the large image is converted to a zoomable image usinig
Google Map API.
Usage:
NULL = genome_map($gb);
Options:
-width image width (default: 8192)
-height image height (default: 8192)
-output "g" for graph, "show" for display (default: "show")
-datafilename coordinate file name (default: "data.coord")
-gmap 1 to create Google Map view, 0 to only generate PNG image
(default:1)
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20071008-01 added -gmap option
20070628-01 added -datafilename option
20070623-01 initial posting |
Name: plasmid_map - draws circular map of the genome
Description:
This method creates a circular map of the genome using SVG,
suitable for plasmids and circular bacterial chromosomes.
Usage:
NULL = plasmid_map($gb);
Options:
-ptt ptt file name
-output g|show (default:show)
-filename output file name (default:plasmid_map.svg)
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20071023-01 fixed SVG-related bug
20020905-01 initial posting |
Name: seq2png - converts a sequence to PNG image
Description:
Converts a sequence to a png image, by representing nucleotide
sequences with representative pixels.
A is shown in red, T is shown in green,
G is shown in yellow, and C is shown in blue.
Usage:
NULL = seq2png(G instance);
Options:
-width width of the image (default:640)
-window window size of a sequence to represent each pixel (default: 20)
-filename output filename (default:'seq.png')
-output "g" for graph, "show" for display
Author:
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
History:
20060714 added -window option
20010906 update with options
20010830 initial posting |
Methods code
sub circular_map
{ opt_default("gmap"=>1);
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $gmap = opt_val("gmap");
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 = 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 }
);
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 $gcskb = $svg->group(
id => 'gcskew',
style =>
{ 'stroke' => '#ccff66', '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);
open( PWRITER, ">./data/" . $wfile . ".coord" );
my ( $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 => '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() ) {
if ( $gb->{$feature}->{type} eq "gene" and $gb->{$feature}->{direction} eq "direct" ) {
$count_a++;
my $r = 3400;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
if ( $count_a % 2 == 1 ) {
$cdsa->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye"
);
} else {
$cdsb->path(
id => "a" . $count_a,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye"
);
}
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 "gene" and $gb->{$feature}->{direction} eq "complement" ){
$count_b++;
my $r = 3100;
my ( $xs, $ys ) = &get_pos( $gb->{$feature}->{start}, $r, $bp_length );
my ( $xe, $ye ) = &get_pos( $gb->{$feature}->{end}, $r, $bp_length );
if ( $count_b % 2 == 1 ) {
$cdsx->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye"
);
} else {
$cdsy->path(
id => "b" . $count_b,
'd' => "M$xs $ys A$r $r,0,0 1,$xe $ye"
);
}
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" );
}
}
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 $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 $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 );
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 );
$gcska->path( 'd' => "M$px,$py L$x,$y" );
$px = $x;
$py = $y;
$gcskb->path( 'd' => "M$pxg,$pyg L$xg,$yg" );
$pxg = $xg;
$pyg = $yg;
}
$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/" . $wfile . ".svg" );
print WRITER $svg->xmlify;
close WRITER;
if($gmap){
generateGMap("graph/$wfile.svg");
}} | sub dnawalk
{ opt_default("gmap"=>1);
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $name = $gb->{LOCUS}->{id};
my $segments = 10;
my $gmap = opt_val("gmap");
mkdir("data", 0777);
mkdir("graph", 0777);
my ($XX, $YY) = (8192, 8192);
my $im = new GD::Image($XX,$YY);
my $margin = 50;
my ($cds_x, $cds_y);
my ($out, @out);
msg_error("Map generation will take a few minutes. Please make yourself comfortable until the image is generated ;-\)\n\n") if ($gmap);
my $black = $im->colorAllocate(0 ,0 ,0 );
my $white = $im->colorAllocate(255,255,255);
my $momo = $im->colorAllocate(255,127,127);
my $h_p = $im->colorAllocate(255,127,191);
my $s_p = $im->colorAllocate(255,127,255);
my $ppl = $im->colorAllocate(191,127,255);
my $h_b = $im->colorAllocate(127,127,255);
my $s_b = $im->colorAllocate(127,191,255);
my $ss_b = $im->colorAllocate(127,255,255);
my $s_g = $im->colorAllocate(127,255,191);
my $h_g = $im->colorAllocate(127,255,127);
my $g_y = $im->colorAllocate(191,255,127);
my $sb_y = $im->colorAllocate(255,255,127);
my $p_y = $im->colorAllocate(255,191,127);
my $black = $im->colorAllocate(0, 0, 0, );
my @colors = ($momo, $h_p, $s_p, $ppl, $h_b, $s_b, $ss_b, $s_g, $h_g, $g_y);
my ( $x, $y, $color ) = ( 0, 0, $black );
my ( @pos_x, @pos_y) ;
my $nuc;
for (my $i=0; $i<=$segments; $i++){
my $tmpseq = substr( $gb->{SEQ}, $i * int(length($gb->{SEQ})/$segments), int(length($gb->{SEQ})/$segments) );
$tmpseq =~ tr[atgc][0286];
foreach my $word (split(//, $tmpseq)){
$nuc++;
if($word < 5){
$y += ($word - 1);
}else{
$x += ($word - 7);
}
push (@pos_x, $x);
push (@pos_y, $y);
}
}
my $walk_width = max(@pos_x) - min(@pos_x);
my $walk_height = max(@pos_y) - min(@pos_y);
my $compress;
my ($cx, $cy);
if( $walk_width > $walk_height ){
$compress = $walk_width / (8192 - $margin);
if( $compress < 1 && $compress > 0 ){
$compress = 1;
$cx = int (-min(@pos_x)/ $compress + ( 8192 - $walk_width/$compress) / 2);
$cy = int (-min(@pos_y)/ $compress + ( 8192 - $walk_height/$compress)/ 2) ;
}else{
$cx = int (- min(@pos_x) / $compress) + $margin/2;
$cy = int (- min(@pos_y) / $compress + ( 8192 - $walk_height/$compress) / 2);
}
}else{
$compress = $walk_height / (8192 - $margin);
if( $compress < 1 && $compress > 0 ){
$compress = 1;
$cx = int (-min(@pos_x)/ $compress + ( 8192 - $walk_width/$compress) / 2);
$cy = int (-min(@pos_y)/ $compress + ( 8192 - $walk_height/$compress)/ 2) ;
}else{
$cx = int (-min(@pos_x)/ $compress + ( 8192 - $walk_width/$compress) / 2);
$cy = int (-min(@pos_y) / $compress) +$margin/2;
}
}
$im->line(0, $cy, 8192, $cy, $white);
$im->line($cx, 0, $cx, 8192, $white);
my $j = 0;
my $k = 0;
for (my $i=0; $i<=length($gb->{SEQ}); $i++){
$j++;
if ($j > length($gb->{SEQ}) / $segments){
$k++;
$j = 0;
}
$color = $colors[$k];
my $xs = int( $cx + $pos_x[$i] / $compress );
my $ys = int( $cy + $pos_y[$i] / $compress );
$im->setPixel( $xs, $ys, $color );} | 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 $before2 = -10000;
while (defined %{$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=>"data.coord", gmap=>1);
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $acnum = $gb->{LOCUS}->{id};
my $datafilename = opt_val("datafilename");
my $output = opt_val("output");
my $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 get_arrow
{ my ( $n, $r, $bp_length ) = @_;
my $rr = 40;
my $rl = 20;
my $x = $cx + ( sin( 2 * $pi * $n / $bp_length ) * $r );
my $y = $cy - ( cos( 2 * $pi * $n / $bp_length ) * $r );
my $th = 2 * $pi * ( 1 + $n ) / $bp_length;
my $xxs = $x - cos($th) * $rr;
my $yys = $y - sin($th) * $rr;
my $xxe = $x + cos($th) * $rr;
my $yye = $y + sin($th) * $rr;
$th -= $pi * 3 / 4;
my $xl = $xxe + cos($th) * $rl;
my $yl = $yye + sin($th) * $rl;
$th -= $pi * 2 / 4;
my $xr = $xxe + cos($th) * $rl;
my $yr = $yye + sin($th) * $rl;
return ( $xxs, $yys, $xxe, $yye, $xl, $yl, $xr, $yr );} | sub get_arrowc
{ my ( $n, $r, $bp_length ) = @_;
my $rr = 40;
my $rl = 20;
my $x = $cx + ( sin( 2 * $pi * $n / $bp_length ) * $r );
my $y = $cy - ( cos( 2 * $pi * $n / $bp_length ) * $r );
my $th = 2 * $pi * ( 1 + $n ) / $bp_length;
my $xxs = $x - cos($th) * $rr;
my $yys = $y - sin($th) * $rr;
my $xxe = $x + cos($th) * $rr;
my $yye = $y + sin($th) * $rr;
$th -= $pi * 1 / 4;
my $xl = $xxs + cos($th) * $rl;
my $yl = $yys + sin($th) * $rl;
$th += $pi * 2 / 4;
my $xr = $xxs + cos($th) * $rl;
my $yr = $yys + sin($th) * $rl;
return ( $xxs, $yys, $xxe, $yye, $xl, $yl, $xr, $yr );} | sub get_mapp
{ my ( $n, $r, $bp_length ) = @_;
my $x = $n * 8192 / 8000;
my $y = $r * 8192 / 8000;
return ( $x, $y );} | sub get_pos
{ my ( $n, $r, $bp_length ) = @_;
my $x = $cx + ( sin( 2 * $pi * $n / $bp_length ) * $r );
my $y = $cy - ( cos( 2 * $pi * $n / $bp_length ) * $r );
return ( $x, $y );} | sub get_posp
{ my ( $n, $r, $bp_length ) = @_;
my $x = $cx + ( sin( 2 * $pi * $n / 100 ) * $r );
my $y = $cy - ( cos( 2 * $pi * $n / 100 ) * $r );
return ( $x, $y );} | 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;} | sub seq2png
{ &opt_default(width=>640, filename=>"seq.png", output=>"show", window=>"20");
my @args = opt_get(@_);
my $gb = opt_as_gb(shift @args);
my $width = opt_val("width");
my $window = opt_val("window");
my $output = opt_val("output");
my $filename = opt_val("filename");
my $height = int((length($gb->{SEQ})/$window)/$width)+1;
my $im = new GD::Image($width, $height);
my $white = $im->colorAllocate(255,255,255);
my $red = $im->colorAllocate(255,0,0);
my $yellow = $im->colorAllocate(255,255,0);
my $green = $im->colorAllocate(0,150,0);
my $blue = $im->colorAllocate(0,0,255);
my ($x, $y);
my $count = 0;
for ($y = 0; $y <= $height; $y ++){
for ($x = 0; $x <= $width; $x ++){
my $color=$white;
my $g = substr($gb->{SEQ}, $count * $window, $window) =~ tr/g/g/;
my $c = substr($gb->{SEQ}, $count * $window, $window) =~ tr/c/c/;
my $a = substr($gb->{SEQ}, $count * $window, $window) =~ tr/a/a/;
my $t = substr($gb->{SEQ}, $count * $window, $window) =~ tr/t/t/;
if($g >= $c && $g >= $a && $g >= $t){
$color=$yellow;
}elsif($c >= $g && $c >= $a && $c >= $t){
$color = $blue;
}elsif($a >= $g && $a >= $c && $a >= $t){
$color = $red;
}elsif($t >= $g && $t >= $c && $t >= $a){
$color = $green;
}
$im->setPixel($x,$y,$color);
last if ($count == length($gb->{SEQ}));
$count ++;
}
}
mkdir ('graph', 0777);
open(OUT, '>graph/' . $filename);
binmode OUT;
print OUT $im->png;
close(OUT);
msg_gimv("graph/$filename") if ($output eq 'show');} | General documentation
No general documentation available.