annotate sRNA_rpkm_distribution_along_genome.pl @ 21:9dcffd531c76 draft

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#!/usr/bin/perl -w
#==========================================================================================
# Date: 
# Title: 
# Comment: Program to plot gene structure
# Input: 1. 
#        2. 
#        3. 
# 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,"span=s","c=s","o=s","out=s","l=s","cen:s","n=s","mark=s","h");
if (!( defined $opt{o}) || defined $opt{h}) {
&usage;
}
my $span=$opt{span};
my $sample_cloumn=$opt{n};
my $mark=$opt{mark};
#===============================Define Attribute==========================================
my %attribute=(
	canvas=>{
		'width'=>1500,
		'height'=>1800
	},
	text=>{
		'stroke'=>"#000000",
		'fill'=>"none",
		'stroke-width'=>0.5
	},
	line=>{
		'stroke'=>"black",
		'stroke-width'=>1
	},
	csv=>{
		'stroke'=>"red",
		'stroke-width'=>0.5
	},
	exon=>{
		'stroke'=>"black",
		'stroke-width'=>1
	},
	intron=>{
		'stroke'=>"black",
		'stroke-width'=>1.5
	},
	font=>{
		'fill'=>"#000000",
		'font-size'=>12,
		'font-size2'=>10,
		#'font-weight'=>'bold',
		'font-family'=>"Arial"
		#'font-family'=>"ArialNarrow-bold"
	},
	rect=>{
		'fill'=>"lightgreen",
		'stroke'=>"black",
		'stroke-width'=>0.5
	},
	readwidth=>0.5
);
#############################s#define start coordinate and scale
open(TXT,">$opt{out}");
open(LENGTH,"$opt{l}")||die"cannot open the file $opt{l}";
my %length;
while (my $aline=<LENGTH>) {
	chomp $aline;
	next if($aline=~/^\#/);
	my @temp=split/\t/,$aline;
	$temp[0]=~s/^c/C/;
	$length{$temp[0]}=$temp[1];
}
close LENGTH;
#---------------------------------------------------------------
my %centromere;
if (defined($opt{cen})) {
	open(CEN,"$opt{cen}")||die"cannot open the file $opt{cen}";
	while (my $aline=<CEN>) {
		chomp $aline;
		next if($aline=~/^\#/);
		my @temp=split/\t/,$aline;
		$temp[0]=~s/^c/C/;
		$centromere{$temp[0]}[0]=$temp[1];
		$centromere{$temp[0]}[1]=$temp[2];
	}
	close CEN;
}

#---------------------------------------------------------------
my $max_length=0;
foreach my $chr (keys %length) {
	if ($max_length<$length{$chr}) {
		$max_length=$length{$chr};
	}
	print "$chr\n";
}
#====================================cluster data=======================================
open(CLUSTER,"$opt{c}")||die"cannot open the file $opt{c}";
my %cluster;
my %cluster_density;
#my @sample=qw(39B3 3PA3 3LC3);
my @cluster_non_add;
while (my $aline=<CLUSTER>) {
	next if($aline=~/^\#/);
	chomp $aline;##ID	chr	strand	start	end	19B1
	my @temp=split/\t/,$aline;
	my @ID=split/\:/,$temp[0];
	my @posi=split/\-/,$ID[1];
	push @{$cluster{$ID[0]}},[$temp[0],$posi[0],$posi[1],$temp[2+$sample_cloumn]];#ID	start	end	rpkm(19B1,1PA1,1LC1);
}
close CLUSTER;
my %max_cluster;
foreach my $chr (sort keys %cluster) {
#	for (my $i=0;$i<3 ;$i++) {
#		$max_cluster{$chr}[$i]=0;
#	}	
	$max_cluster{$chr}=0
}
foreach my $chr (sort keys %cluster) {
	@{$cluster{$chr}}=sort{$a->[1] <=> $b->[1]}@{$cluster{$chr}};
	#for (my $s=0;$s<3;$s++) {
		for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
			if ($cluster{$chr}[$i][3]>$max_cluster{$chr}) {
				$max_cluster{$chr}=$cluster{$chr}[$i][3];
			}
		}
	#}

}
#---------------------------------------------------------------------------------------
foreach my $chr(keys %cluster) {
	for(my $i=0;$i<$#{$cluster{$chr}};$i++) {
		my $start=int($cluster{$chr}[$i][1]/$span);
		my $end=int($cluster{$chr}[$i][2]/$span);
		if ($start==$end) {
			#for (my $j=0;$j<3 ;$j++) {
				$cluster_density{$chr}[$start]+=$cluster{$chr}[$i][3];
			#}
		
		}
		else{
			for (my $m=$start;$m<=$end ;$m++) {
				#for (my $j=0;$j<3 ;$j++) {
					$cluster_density{$chr}[$m]+=$cluster{$chr}[$i][3];
				#}
			}
		}
	}
}
my %max_cluster_density;
foreach my $chr (sort keys %cluster) {#
	#for (my $i=0;$i<3 ;$i++) {
		for (my $i=0;$i<$#{$cluster{$chr}} ;$i++) {
			$max_cluster_density{$chr}=0;
		}
	#}	
}
foreach my $chr (sort keys %cluster) {
	#for (my $i=0;$i<3;$i++) {
		for (my $k=0;$k<$#{$cluster_density{$chr}} ;$k++) {
			if (!(defined($cluster_density{$chr}[$k]))) {
				$cluster_density{$chr}[$k]=0;
			}
			if ($cluster_density{$chr}[$k]>$max_cluster_density{$chr}) {
				$max_cluster_density{$chr}=$cluster_density{$chr}[$k];
			}
			print TXT "$chr\t$k\t$cluster_density{$chr}[$k]\n";
		}	
	#}
}
#--------------------------------------------------------------------
my $XOFFSET=50;
my $YOFFSET=60;
#my $length=$end-$start+1;
my $Xscale=600/$max_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
#my $high_cov=$high_cov9B1=0.5;#定义峰图最高峰
#my $Yscale=1/$high_cov;#定义Y轴比例尺 1:60 y轴的坐标长度都要按照此比例尺换算
#========================================New canvas============================
####    Starting    ####
#新建画布
my $svg=SVG->new();
#画图起始点
my $canvas_start_x=$XOFFSET;
my $canvas_end_x=$XOFFSET+$max_length*$Xscale;#按照比例尺 画线
my $canvas_start_y=$YOFFSET;
my $canvas_end_y=$YOFFSET;

my $chr_width=$YOFFSET;
my $chr_start_y;
my $chr_end_y;
my $Yscale=0.01;
foreach my $chr (sort keys %length) {
	my $chr_start_x=$XOFFSET;
	my $chr_end_x=$XOFFSET+$length{$chr}*$Xscale;
	$chr_start_y+=$chr_width;
	$chr_end_y+=$chr_width;
	$svg->line(x1=>$chr_start_x,y1=>$chr_start_y,x2=>$chr_end_x,y2=>$chr_end_y,'stroke',$attribute{line}{'stroke'},'stroke-width',$attribute{line}{'stroke-width'});
	$svg->text('x',$XOFFSET-40,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$chr);
	$svg->text('x',$chr_end_x+20,'y',$chr_start_y,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',$length{$chr});
	

	if (defined($centromere{$chr}[0])) {
		$svg->rect('x',$XOFFSET+$centromere{$chr}[0]*$Xscale,'y',$chr_start_y,'width',($centromere{$chr}[1]-$centromere{$chr}[0]+1)*$Xscale,'height',5,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
	}
	for (my $i=0;$i<$#{$cluster_density{$chr}} ;$i++) {
		if ($cluster_density{$chr}[$i]*$Yscale>40) {
			$cluster_density{$chr}[$i]=40/$Yscale;
			$svg->rect('x',$XOFFSET+$i*$span*$Xscale,'y',$chr_start_y-45,'width',$span*$Xscale,'height',5,'stroke',"green",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"green");
		}
		my $cluster_density_start_x=$XOFFSET+$i*$span*$Xscale;
		my $cluster_density_end_x=$XOFFSET+($i+1)*$span*$Xscale;
		my $cluster_density_start_y=$chr_start_y-$cluster_density{$chr}[$i]*$Yscale;
		#my $cluster_density_end_y=$chr_start_y-$cluster_density{$chr}[$i+1][0]*$Yscale;
		#$svg->line('x1',$cluster_density_start_x,'y1',$cluster_density_start_y,'x2',$cluster_density_end_x,'y2',$cluster_density_end_y,'stroke',"red",'stroke-width',$attribute{csv}{'stroke-width'});
		$svg->rect('x',$cluster_density_start_x,'y',$chr_start_y-$cluster_density{$chr}[$i]*$Yscale,'width',$span*$Xscale,'height',$cluster_density{$chr}[$i]*$Yscale,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red");
	}
	
	$chr_width=50;
	
	#$svg->rect('x',$c_non_add_start_x,'y',$c_non_add_start_y,'width',$cluster_non_add_width,'height',$cluster_non_add_heigth,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
}

my $span_k=$span/1000;
$svg->text('x',200,'y',$chr_start_y+20,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"$mark sRNA rpmk \/ $span_k kb");

$svg->rect('x',600,'y',500,'width',10,'height',10,'stroke',"red",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"red");
$svg->text('x',620,'y',510,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"sRNA rpkm");

if (defined($opt{cen})) {
	$svg->rect('x',600,'y',520,'width',10,'height',10,'stroke',"blue",'stroke-width',$attribute{intron}{'stroke-width'},'fill',"blue");
	$svg->text('x',620,'y',530,'style','fill:black;text-anchor:left','stroke',$attribute{text}{'stroke'},'stroke-width',$attribute{text}{'stroke-width'},'font-size',12,'font-family',$attribute{font}{'font-family'},'-cdata',"centromere");
}

close TXT;
open (OUT,">$opt{o}");
print OUT $svg->xmlify();

sub log2 {
	my $n = shift;
	return log($n)/log(2);
}

sub usage{
print <<"USAGE";
Version $version
Usage:
$0 
options:
-span
-n sample cloumn
-mark sample name
-o output graph file name with html or svg extension
-c cluster file input
-out txt output
-l length of chr
-cen centromere
-h help
USAGE
exit(1);
}