tools/svg/synteny/draw_synteny_OO.pl

   1 #!/bin/env perl
   2
   3 =head1 Name
   4
   5 draw_synteny_OO.pl  --  draw synteny figure between two sequences (OO version)
   6
   7 =head1 Description
   8
   9 draw linear figures for synteny analysis with nucmer result,
  10 also add gene and TE elements to svg figure.
  11
  12 =head1 Version
  13
  14   Author: Hu Xuesong, huxuesong@genomics.org.cn
  15   Version: 1.0,  Date: 2009-12-14
  16
  17 =head1 Usage
  18
  19   perl draw_synteny_parallel_melon4.pl [options]
  20   --width <int>         set the image width (1200)
  21   --height <int>        set the image height (720)
  22   --chr <file>          set the chromosome length file
  23   --list <file>         set the pairwise relation list file
  24 //  --scale <int>         set the unit for big scales
  25 //  --resolution <float>  set the figure resolution, default 100000
  26   --synteny_heigth <int>  set the height of each unit of synteny figure, default=60
  27   --gene1 <file>         draw exon-intron structure for one gene set
  28   --gene2 <file>         draw exon-intron structure for another gene set
  29   --TE1 <file>           draw colorful blocks for one TE set
  30   --TE2 <file>           draw colorful blocks for another TE set
  31   --contig1 <file>               draw contigs for one scaffold set
  32   --contig2     <file>           draw contigs for another scaffold set
  33   --outdir <str>        set the output directory
  34   --verbose   output verbose information to screen
  35   --help      output help information to screen
  36
  37 =head1 Exmple
  38
  39   perl draw_synteny_OO.pl  --synteny_heigth 150 --scale 10000 --resolution 100 -chr ./melon_cucumber_chrs.list --list ./melo_4BACs.delta.filter.coords.list --gene1 ./melo_4BACs.gbk.noTE.gff -TE1 ./melo_4BACs.fa.TE.gff --gene2 ./cucumber.3scaffs.gene.gff.need.noTE.gff --TE2 ./cucumber.scaffs.TE.gff
  40
  41 =cut
  42
  43 use strict;
  44 use warnings;
  45 use Getopt::Long;
  46 use FindBin qw($Bin $Script);
  47 use File::Basename qw(basename dirname);
  48 use Data::Dumper;
  49 use lib "$Bin/../lib";
  50 use lib 'U:\dev\sda\5\develop\ActivePerl510\Perl64\site\lib\\';
  51 use SVG;
  52 use FontSize;
  53
  54 #my $figure_resolution; ##one point stands for 10000 bp
  55 #my $big_scale;
  56 my ($synteny_heigth);
  57 my ($Gene1_file,$TE1_file,$Gene2_file,$TE2_file,$contig1_file,$contig2_file,$depth_file,$img_width,$img_height);
  58 my ($pairwise_file,$chr_len_file1);
  59 my ($Verbose,$Help,$Outdir);
  60 GetOptions(
  61         "width:i"=>\$img_width,
  62         "height:i"=>\$img_height,
  63         "chr:s"=>\$chr_len_file1,
  64         "list:s"=>\$pairwise_file,
  65 #       "scale:i"=>\$big_scale,
  66 #       "resolution:f"=>\$figure_resolution,
  67         "synteny_heigth:i"=>\$synteny_heigth,
  68         "gene1:s"=>\$Gene1_file,
  69         "gene2:s"=>\$Gene2_file,
  70         "TE1:s"=>\$TE1_file,
  71         "TE2:s"=>\$TE2_file,
  72         "contig1:s"=>\$contig1_file,
  73         "contig2:s"=>\$contig2_file,
  74         "outdir:s"=>\$Outdir,
  75         "verbose"=>\$Verbose,
  76         "help"=>\$Help
  77 );
  78 $img_width ||=1200;
  79 $img_height ||=720;
  80 #$figure_resolution ||= 100000;
  81 #$big_scale ||= 10000000;
  82 $synteny_heigth ||= 60;
  83 $Outdir ||= ".";
  84 die `pod2text $0` if (!$chr_len_file1 || !$pairwise_file || $Help);
  85
  86 #Contig_4       1       97799   scaffold375     1       34612   -
  87 #Contig_4       1       97799   scaffold2282    377     67038   +
  88 sub read_chromosome_file($$) {
  89         my $chromosome_file=shift;
  90         my $chromosome_p=shift;
  91         open CHR,$chromosome_file or die "[x]$!";
  92         while(<CHR>) {
  93                 chomp;
  94                 next if $_=~/^chr_id\t/;
  95                 s/^\s+//;
  96                 next if(!$_);
  97                 my @t = split /\s+/;
  98                 push @{$chromosome_p->{$t[0]}}, \@t;
  99         }
 100         close CHR;
 101 }
 102
 103 #Contig_1_4     Contig_1        -       79705   59416   scaffold629_4   scaffold629     +       2529462 2550090
 104 #Contig_2_5     Contig_2        +       1       6619    scaffold421_5   scaffold421     +       290060  296703
 105 sub read_pairwise_file {
 106         my $pairwise_file = shift;
 107         my $synteny_p = shift;
 108         open IN, $pairwise_file || die "[x]Fail open $pairwise_file !";
 109         while (<IN>) {
 110                 chomp;
 111                 my ($gene1,$chr1,$strand1,$start1,$end1,$gene2,$chr2,$strand2,$start2,$end2) = split /\s+/;
 112                 push @$synteny_p,[$gene1,$start1,$end1,$strand1,$gene2,$start2,$end2,$strand2,$chr1,$chr2];
 113         }
 114         close IN;
 115 }
 116
 117 #Contig_8       BGI     mRNA    10453   11903   .       +       .       ID=Apl_00006;
 118 #Contig_8       BGI     CDS     10453   10464   .       +       0       Parent=Apl_00006;
 119 #Contig_8       BGI     CDS     11887   11903   .       +       0       Parent=Apl_00006;
 120 sub read_gene_gff($$) {
 121         my $file=shift;
 122         my $ref=shift;
 123         open (IN,$file) || die ("[x]Fail open $file !\n");
 124         while (<IN>) {
 125                 chomp;
 126                 s/^\s+//;
 127                 next if(/^\#/);
 128                 my @t = split(/\t/);
 129                 my $tname = $t[0];
 130                 my $qname;
 131                 if ($t[2] eq 'mRNA' || $t[2] eq 'CDS'|| $t[2] eq 'CDs') {
 132                         $qname = $1 if($t[8] =~ /^GenePrediction\s+(\S+)/ || $t[8] =~ /^ID=(\S+?);/ || $t[8] =~ /^Parent=(\S+?);/);
 133                 }
 134                 if ($t[2] eq 'match' || $t[2] eq 'HSP') {
 135                         $qname = $1 if($t[8] =~ /Target\s+\"(\S+)\"/);
 136                 }
 137                 if ($t[2] eq 'mRNA' || $t[2] eq 'match') {
 138                         my $start = $t[3];
 139                         my $end = $t[4];
 140                         my $strand = $t[6];
 141                         $ref->{$tname}{$qname}{strand} = $strand;
 142                         $ref->{$tname}{$qname}{start} = $start;
 143                         $ref->{$tname}{$qname}{end} = $end;
 144                 }
 145                 if ($t[2] eq 'CDS' || $t[2] eq 'HSP'|| $t[2] eq 'CDs') {
 146 #                       print "$tname\t$qname\n";
 147                         push @{$ref->{$tname}{$qname}{exon}}, [$t[3],$t[4]] if(exists $ref->{$tname}{$qname});
 148                 }
 149         }
 150         close(IN);
 151
 152         foreach my $scaff (sort keys %$ref) {
 153                 my $scaff_p = $ref->{$scaff};
 154         #       print Dumper ($ref->{$scaff});
 155                 foreach my $gene (sort keys %$scaff_p) {
 156                 #       print Dumper ($ref->{$scaff});
 157                         my $gene_p = $scaff_p->{$gene};
 158                         my @exon = @{$gene_p->{exon}};
 159                         @exon = reverse @exon if($exon[0][0] > $exon[-1][0]);
 160                         my @new;
 161                         foreach my $p (@exon) {
 162                                 push @new,$p->[0],$p->[1];
 163                         }
 164                         $ref->{$scaff}{$gene}{exon} = \@new;
 165                 }
 166         }
 167 }
 168
 169 ##gff-version 3
 170 #scaffold375    RepeatMasker    Transposon      1       3000    1611    +       .       ID=TE055206;Target=CR1-Y2_Aves 340 1177;Class=LINE/CR1;PercDiv=29.0;PercDel=2.9;PercIns=0.2;
 171 sub read_TE_gff($$) {
 172         my $file=shift;
 173         my $ref=shift;
 174         open (IN,$file) || die ("[x]Fail open $file !\n");
 175         while (<IN>) {
 176                 chomp;
 177                 s/^\s+//;
 178                 next if(/^\#/);
 179                 my @t = split(/\t/);
 180                 my $tname = $t[0];
 181                 my $qname = $1 if($t[8] =~ /^ID=([^;]+);*/);
 182                 my $type = $1 if($t[8] =~ /Class=([^\/;]+)/);
 183                 my $start = $t[3];
 184                 my $end = $t[4];
 185                 my $strand = $t[6];
 186                 $ref->{$tname}{$qname} = [$start,$end,$strand,$type];
 187         }
 188         close(IN);
 189 }
 190
 191 #Contig_4       1       7836
 192 #Contig_4       8956    26732
 193 sub read_contig_list($$) {
 194         my $file=shift;
 195         my $hash_p=shift;
 196         open IN,$file or die "[x]Fail open $file !\n";
 197         while(<IN>) {
 198                 chomp;
 199                 my @ary=split /\t/;
 200                 push @{$hash_p->{$ary[0]}},[$ary[1],$ary[2]];
 201         }
 202         close IN;
 203 }
 204
 205
 206
 207
 208
 209
 210 my $pairwise_file_base = basename($pairwise_file);
 211 $Outdir =~ s/\/$//;
 212 mkdir $Outdir unless (-d $Outdir);
 213
 214 my %Chr1;
 215 my @Synteny;
 216
 217 #$figure_resolution = 1 / $figure_resolution;
 218
 219 my (%SVG,@Show);
 220 my @Order=('Ruler1','mRNA1','TE1','Name1','Bar1','Synteny',
 221         'Bar2','Name2','TE2','mRNA2','Ruler2');
 222 our %Heights=(
 223         Ruler1 => 20,
 224         Ruler2 => 20,
 225         mRNA1 => 15,
 226         mRNA2 => 15,
 227         TE1 => 15,
 228         TE2 => 15,
 229         Name1 => 10,
 230         Name2 => 10,
 231         Bar1 => 15,
 232         Bar2 => 15,
 233         Synteny => $synteny_heigth
 234 );
 235 my $Y_junt=10;
 236 my %toShow=(
 237         Ruler1 => 1,
 238         Ruler2 => 1,
 239         Name1 => 1,
 240         Name2 => 1,
 241         Bar1 => 1,
 242         Bar2 => 1,
 243         Synteny => 1,
 244 );
 245
 246 ##read data into memory
 247 read_chromosome_file($chr_len_file1,\%Chr1);
 248 read_pairwise_file($pairwise_file,\@Synteny);
 249
 250 my (%Gene1,%Gene2,%TE1,%TE2,%contig1,%contig2,%depth);
 251 read_gene_gff($Gene1_file,\%Gene1) if(defined $Gene1_file);
 252 read_gene_gff($Gene2_file,\%Gene2) if(defined $Gene2_file);
 253 read_TE_gff($TE1_file,\%TE1) if(defined $TE1_file);
 254 read_TE_gff($TE2_file,\%TE2) if(defined $TE2_file);
 255 read_contig_list($contig1_file,\%contig1) if(defined $contig1_file);
 256 read_contig_list($contig2_file,\%contig2) if(defined $contig2_file);
 257 ##figure parameters setting
 258 our $font = FontSize->new();
 259 our $font_family = "Arial";
 260 #my $font_size = 24;    # stringHeight = int($size*0.72); => font_size = stringHeight / 0.72
 261 our $x_margin = 20;
 262 my $y_margin = 20;
 263 my $Seq2_junt=1000;
 264
 265 my %Synteny_length_bp;
 266 for my $key (keys %Chr1) {
 267         my ($Seq1_name,$Seq1_start,$Seq1_end) = @{${$Chr1{$key}}[0]};
 268         my $Seq2_lenA = 0;
 269         my $Seq1_len = $Seq1_end - $Seq1_start +1;
 270         for (@{$Chr1{$key}}) {
 271                 my ($Seq1_name,$Seq1_start,$Seq1_end,$Seq2_name,$Seq2_start,$Seq2_end,$Reverse) = @$_;
 272                 #$Seq1_lenA = $Seq1_end - $Seq1_start;
 273                 $Seq2_lenA += $Seq2_junt if $Seq2_lenA;
 274                 $Seq2_lenA += $Seq2_end - $Seq2_start +1;
 275         }
 276         $Synteny_length_bp{$key} = ($Seq1_len >= $Seq2_lenA) ? $Seq1_len : $Seq2_lenA;
 277         my $X_start=0;
 278
 279         # Ruler1
 280         #plot_ruler("svg",$svg,"Y",$backbone2_height + 100 + $y_margin, "X_start",$synteny_Xstart+$X_start,"X_end",$synteny_Xstart+$X_start+$Seq2_len* $figure_resolution,"bp_start",$Seq2_start,"bp_end",$Seq2_end,"scaletype","Kb","scaletypepos","right","scalestart","auto","rulerstyle",2,"bigscalesize",$big_scale);
 281         push @{$SVG{$key}{'Ruler1'}},[0,$Seq1_start,$Seq1_len];
 282
 283         if(defined $contig1_file && exists $contig1{$Seq1_name}) {
 284                 $toShow{'Bar1'}=1;
 285                 for (@{$contig1{$Seq1_name}}) {
 286                         my ($start,$end)=@$_;
 287                         my $str='1: '.$Seq1_name;
 288                         push @{$SVG{$key}{'Bar1'}},[$str,$start-$Seq1_start+1,$end-$start+1,'black'];#($str,$margin+$start,$len,$color)
 289                 }
 290         }
 291
 292         $SVG{$key}{'Name1'}=[[$Seq1_name,0,$Seq1_len]];
 293         if (defined $TE1_file && exists $TE1{$Seq1_name}) {
 294                 $toShow{'TE1'}=1;
 295                 my $Seq1_p = $TE1{$Seq1_name};
 296                 foreach my $TE1_id (sort keys %$Seq1_p) {
 297                         my $TE1_p = $Seq1_p->{$TE1_id}; ##$ref->{$tname}{$qname} = [$start,$end,$strand,$type];
 298                         my ($start,$end,$strand,$type) = @$TE1_p;
 299                         my $str=join(': ',$type,$TE1_id);
 300                         push @{$SVG{$key}{'TE1'}},[$str,$start-$Seq1_start+1,$end-$start+1];#($str,$margin+$start,$len)
 301                         }
 302         }
 303
 304         if (defined $Gene1_file && exists $Gene1{$Seq1_name}) {
 305                 $toShow{'mRNA1'}=1;
 306                 my $Seq1_p = $Gene1{$Seq1_name};
 307                         foreach my $gene1_id (keys %$Seq1_p) {
 308                                 my @StartEndStrandFull=($Seq1_p->{$gene1_id}{start}-$Seq1_start+1,$Seq1_p->{$gene1_id}{end}-$Seq1_start+1,$Seq1_p->{$gene1_id}{strand},1);
 309                                 #next if ($StartEndStrand[0] > $Seq1_end or $StartEndStrand[1] < $Seq1_start);
 310                                 if ($StartEndStrandFull[0] < $Seq1_start-$Seq2_junt/2) {
 311                                         $StartEndStrandFull[3]=0;
 312                                         $StartEndStrandFull[0]=$Seq1_start-$Seq2_junt/2;
 313                                 }
 314                                 if ($StartEndStrandFull[1] > $Seq1_end+$Seq2_junt/2) {
 315                                         $StartEndStrandFull[3]=0;
 316                                         $StartEndStrandFull[1]=$Seq1_end+$Seq2_junt/2;
 317                                 }
 318                                 my @exon = @{$Seq1_p->{$gene1_id}{exon}};
 319                                 #my $gene1_strand = $Seq1_p->{$gene1_id}{strand};
 320                                 my @X_exon;
 321                                 #push @X_exon,$_-$Seq1_start+1 for (@exon);
 322                                 for (@exon) {
 323                                         my $pos=$_-$Seq1_start+1;
 324                                         $pos=-$Seq2_junt/2 if $pos<-$Seq2_junt/2;
 325                                         $pos=$Seq1_end+$Seq2_junt/2 if $pos>$Seq1_end+$Seq2_junt/2;
 326                                         push @X_exon,$pos;
 327                                 }
 328                                 push @{$SVG{$key}{'mRNA1'}},[$gene1_id,\@StartEndStrandFull,\@X_exon];
 329                         }
 330                 }
 331
 332         my $count2=0;
 333         for (@{$Chr1{$key}}) {
 334                 ++$count2;
 335                 my ($Seq1_name,$Seq1_start,$Seq1_end,$Seq2_name,$Seq2_start,$Seq2_end,$Reverse) = @$_;
 336                 #my $Seq1_len = $Seq1_end - $Seq1_start +1;
 337                 my $Seq2_len = $Seq2_end - $Seq2_start +1;
 338                 push @{$SVG{$key}{'Ruler2'}},[$X_start,$Seq2_start,$Seq2_len];
 339                 #$SVG{$key}{'Name1'}=[[$Seq1_name,0,$Seq1_len]];
 340                 push @{$SVG{$key}{'Name2'}},[$Seq2_name,$X_start,$Seq2_len];
 341
 342 # »¹Ã»¿¼ÂÇ¸ºÁ´¡¡
 343         if(defined $contig2_file && exists $contig2{$Seq2_name}) {
 344                 $toShow{'Bar2'}=1;
 345                 for (@{$contig2{$Seq2_name}}) {
 346                         my ($start,$end)=@$_;
 347                         my $str="$count2: $Seq2_name";
 348                         push @{$SVG{$key}{'Bar2'}},[$str,$X_start+$start-$Seq2_start+1,$end-$start+1,'black'];#($str,$margin+$start,$len,$color)
 349                 }
 350         }
 351
 352                 if (defined $TE2_file && exists $TE2{$Seq2_name}) {
 353                         $toShow{'TE2'}=1;
 354                         my $Seq2_p = $TE2{$Seq2_name};
 355                         foreach my $TE2_id (sort keys %$Seq2_p) {
 356                                 my $TE2_p = $Seq2_p->{$TE2_id}; ##$ref->{$tname}{$qname} = [$start,$end,$strand,$type];
 357                                 my ($start,$end,$strand,$type) = @$TE2_p;
 358                                 next if ($end<$Seq2_start or $start>$Seq2_end);
 359                                 my $str=join(': ',$type,$TE2_id);
 360                                 my $len=$end-$start+1;
 361                                 if ($Reverse eq "-") {
 362                                         $start = $Seq2_end - $end +1;
 363                                 }
 364                                 my $begin=$start-$Seq2_start+1;
 365                                 if ($begin<-$Seq2_junt/3) {
 366                                         $len += $begin+$Seq2_junt/3;
 367                                         $begin=-$Seq2_junt/3;
 368                                 }
 369                                 push @{$SVG{$key}{'TE2'}},[$str,$X_start+$begin,$len];
 370                         }
 371
 372                 }
 373
 374
 375                 $X_start += $Seq2_len + $Seq2_junt;
 376         }
 377 }
 378
 379 our $WidthPoint;
 380 our $HeightPoint;
 381 for (@Order) {
 382         if (defined $toShow{$_}) {
 383                 push @Show,$_;
 384                 $HeightPoint += $Heights{$_} + $Y_junt;
 385         }
 386 }
 387 $HeightPoint -= $Y_junt;
 388 $HeightPoint = ($img_height-2*$y_margin)/$HeightPoint;
 389 our ($Y_start,$svg);
 390 #our $MaxLenBP;
 391 my $Ln10=2.30258509299405;
 392 my $Lg2=0.301029995663981;
 393 my $Lg5=0.698970004336019;
 394 our $OTF;       # One,Two,Five
 395 our ($cStepN,$cStepKMGT,$cStepKMGTn);   # cent. step
 396
 397 for my $key (keys %SVG) {
 398         my $MaxLenBP = $Synteny_length_bp{$key};
 399         my $LG_MaxLenBP = log($MaxLenBP)/$Ln10;
 400         $WidthPoint = ($img_width-2*$x_margin)/$MaxLenBP;
 401         # for Ruler
 402         my $LG_Main=int($LG_MaxLenBP);
 403         my $LG_suf=$LG_MaxLenBP-$LG_Main;
 404         $cStepN=$LG_Main-1;
 405         if ($LG_suf==0) { $OTF=1; }
 406         elsif ($LG_suf<=$Lg2) { $OTF=2; }
 407         elsif ($LG_suf<=$Lg5) { $OTF=5; }
 408         elsif ($LG_suf<=1) { $OTF=10;$cStepN=$LG_Main; }
 409         else { $OTF=20;$cStepN=$LG_Main; }      # impossible
 410 =pod
 411         if ($cStepN>=24) {$cStepKMGT='Y';$cStepKMGTn=1000000000000000000000000;}
 412         elsif ($cStepN>=21) {$cStepKMGT='Z';$cStepKMGTn=1000000000000000000000;}
 413         elsif ($cStepN>=18) {$cStepKMGT='E';$cStepKMGTn=1000000000000000000;}
 414         elsif ($cStepN>=15) {$cStepKMGT='P';$cStepKMGTn=1000000000000000;}
 415         els
 416 =cut No Genome can larger than 1P. Human only 3G.
 417         if ($cStepN>=12) {$cStepKMGT='T';$cStepKMGTn=1000000000000;}
 418         elsif ($cStepN>=9) {$cStepKMGT='G';$cStepKMGTn=1000000000;}
 419         elsif ($cStepN>=6) {$cStepKMGT='M';$cStepKMGTn=1000000;}
 420         elsif ($cStepN>=3) {$cStepKMGT='K';$cStepKMGTn=1000;}
 421         else {$cStepKMGT='';$cStepKMGTn=1;}
 422         $cStepN=$OTF*10^($LG_Main-2);
 423
 424         $svg = SVG->new('width',$img_width,'height',$img_height);
 425 $svg->rect('x',0,'y',$img_height/2,'height',$y_margin,'width',$img_width,'fill','black');
 426 $svg->rect('x',$x_margin,'y',$y_margin,'height',$img_height-2*$y_margin,'width',$img_width-2*$x_margin,'stroke','black','fill','rgb(196,196,196)');
 427         $Y_start=$y_margin;
 428         open OUT, ">$Outdir/$key.synteny.svg" || die "[x]Fail create $!";
 429         for my $ss (@Show) {
 430                 no strict 'refs';
 431                 $ss =~ /^([^\d]+)(\d)$/;
 432                 my $Func='SVG_'.$1;
 433                 my $OE=($2==2);
 434                 &$Func($ss,$_,$OE) for (@{$SVG{$key}{$ss}});
 435                 $Y_start += ($Y_junt + $Heights{$ss})*$HeightPoint;
 436         }
 437         $svg->rect('x',0,'y',0,'height',$img_height,'width',$x_margin/2,'fill','white');
 438         $svg->rect('x',$img_width-$x_margin/2,'y',0,'height',$img_height,'width',$x_margin/2,'fill','white');
 439         print OUT $svg->xmlify();
 440         close OUT;
 441 }
 442 print "$WidthPoint,$HeightPoint,$svg\n";
 443 sub SVG_Name($$$) {
 444 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 445         my ($str,$margin,$len)=@{$_[1]};
 446         my $height=$Heights{$_[0]}*$HeightPoint;#*.8;
 447         #my $OE=$_[2];
 448         my $Y0=$Y_start+$_[2]*$Heights{$_[0]}*$HeightPoint;#*.8;
 449         my $font_size = int($height / .72);
 450         my $name_width = $font->stringWidth($font_family,$font_size,$str);
 451 #$name_width=0;
 452         my $x=$x_margin+(($len+$margin+$margin)*$WidthPoint-$name_width)/2;
 453         $svg->text('x',$x,'y',$Y0+$height*(!$_[2]),'-cdata',$str,'font-family',$font_family,'font-size',$font_size);
 454 #$svg->line('x1',$x_margin,'y1',$Y_start,'x2',$x+$name_width/2,'y2',$Y0,'stroke','#000000','stroke-width',1);
 455         print "$_[0],$str,$margin,$len\t$Y_start\t$name_width,$font_size\n";
 456 }
 457
 458 sub SVG_Ruler($$) {
 459 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 460 ### Use $WidthPoint; $MaxLenBP; $cStepN,$cStepKMGT,$cStepKMGTn
 461         my ($margin,$start,$len)=@{$_[1]};
 462         my $height=$Heights{$_[0]}*$HeightPoint;
 463         my $g = $svg->group();
 464         my $y=$Y_start+$height/2;
 465         my $x1=$x_margin+($start+$margin)*$WidthPoint;
 466         $g->line('x1',$x1,'y1',$y,'x2',$x1+$len*$WidthPoint,'y2',$y,'stroke','black','stroke-width',$height/16);
 467         my $PosBP=$start;
 468         my $h=$height/8;
 469         while ($PosBP<=$len) {
 470                 my $x=$x_margin+($PosBP+$margin)*$WidthPoint;
 471                 $g->line('x1',$x,'y1',$y,'x2',$x,'y2',$y+$h,'stroke','red','stroke-width',$height/16);
 472
 473                 $PosBP += $cStepN*100;
 474         }
 475 }
 476 sub SVG_mRNA($$) {
 477 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 478 #[$gene1_id,\@StartEndStrand,\@X_exon];
 479         my ($str,$SESFrefA,$EXONrefA)=@{$_[1]};
 480         my $height=$Heights{$_[0]}*$HeightPoint;
 481         my $M_Height=$Heights{$_[0]}*.824;
 482         $M_Height = $Y_junt if $M_Height > $Y_junt;
 483         $M_Height *= .75;
 484         my $font_size = int($M_Height*$HeightPoint / .72);
 485         my $M_str=($$SESFrefA[3] == 1)?'M':'m';
 486         my $M_width = $font->stringWidth($font_family,$font_size,$M_str);
 487         my $Y0=$Y_start+( (!$_[2])*$Heights{$_[0]} + $M_Height*2*(.5-$_[2]) )*$HeightPoint;
 488         my $g = $svg->group('id'=>$str,'onclick',"alert('$str')");
 489         # Bone Line
 490         my $y=$Y_start+$height/2;
 491         my $x1=$x_margin+$$SESFrefA[0]*$WidthPoint;
 492         my $x2=$x_margin+$$SESFrefA[1]*$WidthPoint;
 493         $g->line('x1',$x1,'y1',$y,'x2',$x2,'y2',$y,'stroke','rgb(0,96,196)','stroke-width',$height/4);
 494         # Exon Boxes
 495         while (@$EXONrefA > 1) {
 496                 my $x1=shift @$EXONrefA;
 497                 my $x2=shift @$EXONrefA;
 498                 my $w=$x2-$x1;
 499                 $x1 *= $WidthPoint;     $w *= $WidthPoint;
 500                 $w=1 if $w<1;
 501                 $x1 += $x_margin;
 502                 $g->rect('x',$x1, 'y',$Y_start,'width',$w,'height',$height,'fill','rgb(0,96,96)');
 503         }
 504         # M
 505         my $A_PointX;
 506         if ($$SESFrefA[2] eq '+') {
 507                 $A_PointX=$x2;
 508                 $A_PointX=$img_width-$x_margin/2 if $A_PointX>$img_width-$x_margin/2;
 509                 $A_PointX -= $M_width;
 510         } else {
 511                 $A_PointX=$x1;
 512                 $A_PointX=$x_margin/2 if $A_PointX<$x_margin/2;
 513         }
 514         $g->text('x',$A_PointX,'y',$Y0,'-cdata',$M_str,'font-family',$font_family,'font-size',$font_size);
 515 }
 516 sub SVG_TE($$) {
 517 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 518         my ($str,$start_margin,$len)=@{$_[1]};
 519         my $height=$Heights{$_[0]}*$HeightPoint;
 520         my $x=$x_margin+$start_margin*$WidthPoint;
 521         my $w=$len*$WidthPoint;
 522         $w=1 if $w<1;
 523         $svg->rect('x',$x, 'y',$Y_start,'width',$w,'height',$height,'fill','red','onclick',"alert('$str')");
 524 }
 525 sub SVG_Bar($$) {
 526 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 527 #($str,$margin+$start,$len,$color)
 528         my ($str,$start_margin,$len,$color)=@{$_[1]};
 529         my $height=$Heights{$_[0]}*$HeightPoint;
 530         my $x=$x_margin+$start_margin*$WidthPoint;
 531         my $w=$len*$WidthPoint;
 532         $w=1 if $w<1;
 533         $svg->rect('x',$x, 'y',$Y_start,'width',$w,'height',$height,'fill',$color,'onclick',"alert('$str')");
 534 }
 535 sub SVG_Synteny($$) {
 536 $svg->rect('x',$x_margin, 'y',$Y_start,'width',$img_width-2*$x_margin,'height',$Heights{$_[0]}*$HeightPoint,'fill','none','stroke','blue');
 537 }