diff Length_Distibution.pl @ 19:e0884a4b996b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Length_Distibution.pl	Wed Nov 05 01:17:26 2014 -0500
@@ -0,0 +1,219 @@
+#!/usr/bin/perl -w
+#==========================================================================================
+# Date: 
+# Title: 
+# Comment: Program to plot gene structure
+# Input: 1. input file of Gene region annotation which format like GenePred
+#        2. input file of Transcripts region annotation which format like GenePred
+#        3. input file of gene snp detail info
+# Output: output file of gene structure graph by html or svg formt
+# Test Usage: 
+#========================================================================================
+#use strict;
+my $version=1.00;
+use SVG;
+use Getopt::Long;
+my %opt;
+GetOptions(\%opt,"i=s","o=s",,"h");
+if (!(defined $opt{i} and defined $opt{o}) || defined $opt{h}) {
+&usage;
+}
+#===============================Define Attribute==========================================
+my %attribute=(
+	canvas=>{
+		'width'=>1500,
+		'height'=>1800
+	},
+	text=>{
+		'stroke'=>"#000000",
+		'fill'=>"none",
+		'stroke-width'=>0.5
+		#'stroke-width2'=>1
+	},
+	line=>{
+		'stroke'=>"black",
+		'stroke-width'=>1
+	},
+	font=>{
+		'fill'=>"#000000",
+		'font-size'=>12,
+		'font-size2'=>10,
+		'font-weight'=>'bold',
+		'font-family'=>"Arial"
+		#'font-family2'=>"ArialNarrow-bold"
+	},
+	rect=>{
+		'fill'=>"lightgreen",
+		'stroke'=>"black",
+		'stroke-width'=>0.5
+	},
+	readwidth=>0.5
+);
+#my $Xscale=600/$length;#定义X轴比例尺 1:1000 x轴的坐标长度都要按照此比例尺换算
+#========================================data============================
+open(IN,"$opt{i}")||die"cannot open the file $opt{i}";
+my @R_length;
+my @T_length;
+my $R_number=0;
+my $T_number=0;
+my $R_max=0;
+my $T_max=0;
+
+my $title=<IN>;
+chomp $title;
+my @title=split/\t/,$title;
+my @mark=split/\s+/,$title[1];
+my $sample_number=@mark;
+while (my $aline=<IN>) {
+	if ($aline=~/^\s/) {
+		my $T_title=<IN>;
+		chomp $T_title;
+		while (my $a_aline=<IN>) {
+			chomp $a_aline;
+			my @temp=split/\t/,$a_aline;
+			my @number=split/\s+/,$temp[1];
+			for (my $i=0;$i<@number ;$i++) {
+				if ($R_max<$number[$i]) {
+					$R_max=$number[$i];
+				}
+			}
+			push @R_length,[$temp[0],@number];
+			$R_number++;
+		}
+	}
+	else {
+		chomp $aline;
+		my @temp=split/\t/,$aline;
+		my @number=split/\s+/,$temp[1];
+		for (my $i=0;$i<@number ;$i++) {
+			if ($T_max<$number[$i]) {
+				$T_max=$number[$i];
+			}
+		}
+		push @T_length,[$temp[0],@number];
+		$T_number++;
+	}
+}
+close IN;
+print "Tag max: $T_max\nRead max: $R_max\n";
+my $kd_number=5;
+##=======================Reads 纵坐标刻度==========================
+my $r=1;
+my $rr=1;
+my $R=$R_max;
+while ($R>10) {
+	$R=$R/10;
+	$r=$r*10;
+	$rr++;
+}
+$R=int($R+0.5);
+my $R_xg=$R/$kd_number*$r;#纵坐标一小格大小（一共10格）
+my $R_kedu_scale_x=6*$rr;#纵坐标刻度文字
+##=======================Tags 纵坐标刻度==========================
+my $t=1;
+my $tt=1;
+my $T=$T_max;
+while ($T>10) {
+	$T=$T/10;
+	$t=$t*10;
+	$tt++;
+}
+$T=int($T+0.5);
+my $T_xg=$T/$kd_number*$t;#纵坐标一小格大小（一共10格）
+my $T_kedu_scale_x=6*$tt;#纵坐标刻度文字
+
+#############################s#define start coordinate and scale
+my $XOFFSET=50;
+my $YOFFSET=60;
+my $width=800;
+my $heigth=800;
+my $X_width=600;
+#my $height=1600;
+####    Starting    ####
+#新建画布
+my $svg=SVG->new(width=>$width,height=>$heigth);
+####坐标轴
+my $axisL=300;#read 纵坐标长度
+my $x_margin = 50;
+#=========Reads number setting==========================================
+my $Y_R_title=30;#标题的纵向宽度
+my $Y_R_0=$YOFFSET+$axisL+$Y_R_title;
+my $X_R_0=$XOFFSET+$x_margin;
+my $R_Yscale=$axisL/$R_xg/$kd_number;
+my $R_Xscale=$X_width/$R_number/($sample_number+1);
+#=====================================Reads Y axis======================
+$svg->line('x1',$X_R_0,'y1',$Y_R_0,'x2',$X_R_0,'y2',$Y_R_0-$axisL,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+for (my $i=1;$i<$kd_number ;$i++) {
+	$svg->line('x1',$X_R_0-5,'y1',$Y_R_0-$i*$R_xg*$R_Yscale,'x2',$X_R_0,'y2',$Y_R_0-$i*$R_xg*$R_Yscale,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+	$svg->text('x',$X_R_0-$R_kedu_scale_x,'y',$Y_R_0-$i*$R_xg*$R_Yscale+4,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$i*$R_xg);
+}
+#=====================================Reads X axis======================
+$svg->line('x1',$X_R_0,'y1',$Y_R_0,'x2',$X_R_0+$X_width,'y2',$Y_R_0,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+
+#print "$R_number\t$sample_number\n";
+for ($i=0;$i<$R_number ;$i++) {
+	for (my $j=1;$j<$sample_number+1 ;$j++) {
+		my $red=$j/$sample_number*255;
+		$svg->rect('x',$X_R_0+($j+$i*($sample_number+1))*$R_Xscale,'y',$Y_R_0-$R_length[$i][$j]*$R_Yscale,'width',$R_Xscale,'height',$R_length[$i][$j]*$R_Yscale,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
+	}
+	$svg->text('x',$X_R_0+(1+$sample_number/2+$i*($sample_number+1))*$R_Xscale,'y',$Y_R_0+15,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$R_length[$i][0]);
+}
+#===Reads number title
+$svg->text('x',$XOFFSET+400,'y',$YOFFSET,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',"1",'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Reads Length Distribution");
+#===Reads 
+for (my $i=0;$i<$sample_number ;$i++) {
+	my $red=($i+1)/$sample_number*255;
+	$svg->rect('x',$X_R_0+550,'y',$YOFFSET+$Y_R_title+20*$i,'width',15,'height',10,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
+	$svg->text('x',$X_R_0+550+30,'y',$YOFFSET+$Y_R_title+20*$i+10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$i]);
+}
+####==================================================================================
+#=========================================Tag s
+my $Y_T_title=30;#标题的纵向宽度
+my $Y_T_0=$Y_R_0+$axisL+$Y_R_title+50;#length size
+my $X_T_0=$XOFFSET+$x_margin;
+my $T_Yscale=$axisL/$T_xg/$kd_number;
+my $T_Xscale=$X_width/$T_number/($sample_number+1);
+#=====================================Tags Y axis======================
+$svg->line('x1',$X_T_0,'y1',$Y_T_0,'x2',$X_T_0,'y2',$Y_T_0-$axisL,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+for (my $i=1;$i<$kd_number ;$i++) {
+	$svg->line('x1',$X_T_0-5,'y1',$Y_T_0-$i*$T_xg*$T_Yscale,'x2',$X_T_0,'y2',$Y_T_0-$i*$T_xg*$T_Yscale,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+	$svg->text('x',$X_T_0-$T_kedu_scale_x,'y',$Y_T_0-$i*$T_xg*$T_Yscale+4,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$i*$T_xg);
+}
+#=====================================Tags X axis======================
+$svg->line('x1',$X_T_0,'y1',$Y_T_0,'x2',$X_T_0+$X_width,'y2',$Y_T_0,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
+
+#print "$R_number\t$sample_number\n";
+for ($i=0;$i<$T_number ;$i++) {
+	for (my $j=1;$j<$sample_number+1 ;$j++) {
+		my $red=$j/$sample_number*255;
+		$svg->rect('x',$X_T_0+($j+$i*($sample_number+1))*$T_Xscale,'y',$Y_T_0-$T_length[$i][$j]*$T_Yscale,'width',$T_Xscale,'height',$T_length[$i][$j]*$T_Yscale,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
+	}
+	$svg->text('x',$X_T_0+(1+$sample_number/2+$i*($sample_number+1))*$T_Xscale,'y',$Y_T_0+15,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',6,'font-family',$attribute{font}{'font-family'},'-cdata',$T_length[$i][0]);
+}
+#===Reads number title
+$svg->text('x',$XOFFSET+400,'y',$Y_R_0+30+$Y_T_title,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',"1",'font-size',15,'font-family',$attribute{font}{'font-family'},'-cdata',"Tags Length Distribution");
+#===Reads 
+for (my $i=0;$i<$sample_number ;$i++) {
+	my $red=($i+1)/$sample_number*255;
+	$svg->rect('x',$X_T_0+550,'y',$Y_R_0+30+$Y_T_title+20*$i,'width',15,'height',10,'stroke',"black",'stroke-width',"0.5",'fill',"rgb($red,125,0)");
+	$svg->text('x',$X_T_0+550+30,'y',$Y_R_0+30+$Y_T_title+20*$i+10,'style','fill:black;text-anchor:middle','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',10,'font-family',$attribute{font}{'font-family'},'-cdata',$mark[$i]);
+}
+
+
+
+
+open (OUT,">$opt{o}");
+print OUT $svg->xmlify();
+
+sub usage{
+print <<"USAGE";
+Version $version
+Usage:
+$0 
+options:
+-i 
+-o svg output
+-h help
+USAGE
+exit(1);
+}
\ No newline at end of file