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diff html_siRNA.pl @ 0:87fe81de0931 draft default tip

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author bigrna
date Sun, 04 Jan 2015 02:47:25 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/html_siRNA.pl	Sun Jan 04 02:47:25 2015 -0500
@@ -0,0 +1,788 @@
+#!/usr/bin/perl -w
+#Filename:
+#Author: Tian Dongmei
+#Email: tiandm@big.ac.cn
+#Date: 2014-5-29
+#Modified:
+#Description: 
+my $version=1.00;
+
+use strict;
+use Getopt::Long;
+use File::Basename;
+
+my %opts;
+GetOptions(\%opts,"i=s","format=s","o=s","h");
+if (!(defined $opts{o}  and defined $opts{format} and defined $opts{i} ) || defined $opts{h}) { #necessary arguments
+&usage;
+}
+my ($config,$prepath,$rfampath,$genomepath,$clusterpath,$annotatepath,$plotpath,$degpath);
+my ($predir,$rfamdir,$genomedir,$clusterdir,$annotatedir,$plotdir,$degdir);
+open IN,"<$opts{i}";
+$config=<IN>; chomp $config;
+$prepath=<IN>; chomp $prepath;
+$rfampath=<IN>;chomp $rfampath;
+$genomepath=<IN>; chomp $genomepath;
+$clusterpath=<IN>; chomp $clusterpath;
+$annotatepath=<IN>; chomp $annotatepath;
+$plotpath=<IN>; chomp $plotpath;
+my $deg_tag=1;
+if(eof){$deg_tag=0;}
+else{
+	$degpath=<IN>; chomp $degpath;
+}
+close IN;
+my @tmp=split/\//,$prepath;
+$predir=$tmp[-1];
+@tmp=split/\//,$rfampath;
+$rfamdir=$tmp[-1];
+@tmp=split/\//,$genomepath;
+$genomedir=$tmp[-1];
+@tmp=split/\//,$clusterpath;
+$clusterdir=$tmp[-1];
+@tmp=split/\//,$annotatepath;
+$annotatedir=$tmp[-1];
+@tmp=split/\//,$plotpath;
+$plotdir=$tmp[-1];
+
+my $dir=dirname($opts{'o'});
+
+open OUT ,">$opts{'o'}";
+print OUT "<HTML>\n  <HEAD>\n  <TITLE> Analysis Report </TITLE>\n </HEAD>
+ <BODY bgcolor=\"lightgray\">\n  <h1 align=\"center\">\n    <font face=\"ºÚÌå\">\n	<b>Small RNA Analysis Report</b>\n  </font>\n  </h1>
+  <h2>1. Sequence No. and quality</h2>
+  <h3>1.1 Sequece No.</h3>
+";
+
+### raw data no
+open IN,"<$config";
+my @files;my @marks; my @rawNo;
+while (my $aline=<IN>) {
+	chomp $aline;
+	my @tmp=split/\t/,$aline;
+	push @files,$tmp[0];
+	
+	my $no=`less $tmp[0] |wc -l `;
+	chomp $no;
+	if ($opts{'format'} eq "fq" || $opts{'format'} eq "fastq") {
+		$no=$no/4;
+	}
+	else{
+		$no=$no/2;
+	}
+	push @rawNo,$no;
+
+	push @marks,$tmp[1];
+}
+close IN;
+
+### preprocess 
+unless ($prepath=~/\/$/) {
+	$prepath .="/";
+}
+
+my @trimNo;my @collapse;
+my $collapsefile=$prepath."collapse_reads.fa";
+open IN,"<$collapsefile";
+while (my $aline=<IN>) {
+	chomp $aline;
+	<IN>;
+	$aline=~/:([\d|_]+)_x(\d+)$/;
+	my @lng=split/_/,$1;
+	for (my $i=0;$i<@lng;$i++) {
+		if ($lng[$i]>0) {
+			$trimNo[$i] +=$lng[$i];
+			$collapse[$i] ++;
+		}
+	}
+}
+close IN;
+
+my @cleanR;my @cleanT;
+my $clean=$prepath."collapse_reads_18-40.fa";
+open IN,"<$clean";
+while (my $aline=<IN>) {
+	chomp $aline;
+	<IN>;
+	$aline=~/:([\d|_]+)_x(\d+)$/;
+	my @lng=split/_/,$1;
+	for (my $i=0;$i<@lng;$i++) {
+		if ($lng[$i]>0) {
+			$cleanR[$i] +=$lng[$i];
+			$cleanT[$i] ++;
+		}
+	}
+}
+close IN;
+
+my @filterR;my @filterT;
+my $filter=$prepath."collapse_reads_out.fa";
+open IN,"<$filter";
+while (my $aline=<IN>) {
+	chomp $aline;
+	<IN>;
+	$aline=~/:([\d|_]+)_x(\d+)$/;
+	my @lng=split/_/,$1;
+	for (my $i=0;$i<@lng;$i++) {
+		if ($lng[$i]>0) {
+			$filterR[$i] +=$lng[$i];
+			$filterT[$i] ++;
+		}
+	}
+}
+close IN;
+
+
+print OUT "<table border=\"1\">
+<tr align=\"center\">
+<th>&nbsp;</th>
+";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+print  OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Raw Reads No. </th>
+";
+foreach  (@rawNo) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Reads No. After Trimed 3\' adapter </th>
+";
+foreach  (@trimNo) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Unique Tags No. </th>
+";
+foreach  (@collapse) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT  "</tr>
+<tr align=\"center\">
+<th align=\"left\">Clean Reads No. </th>
+";
+foreach  (@cleanR) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Clean Tags No. </th>
+";
+foreach  (@cleanT) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT  "</tr>
+<tr align=\"center\">
+<th align=\"left\">Filter Reads No. \(reads count \>3\) </th>
+";
+foreach  (@filterR) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Filter Tags No. \(reads count \>3\) </th>
+";
+foreach  (@filterT) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>\n</table>";
+print OUT "<p>
+Note:<br />
+The raw data file path is: <b>$files[0]</b><br />
+";
+for (my $i=1;$i<@files;$i++) {
+	print OUT "&nbsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;<b>$files[$i]</b><br />";
+}
+print OUT "The collapsed file path is: <b>$collapsefile</b><br />
+The clean data file path is: <b>$clean</b><br />
+The filter (remain total reads>3) data file path is: <b>$filter</b><br />
+</p>
+<h2> 1. Sequence length count</h2>
+";
+print OUT "\n";
+
+my $length=$prepath."length.html";
+open IN,"<$length";
+while (my $aline=<IN>) {
+	chomp $aline;
+	print OUT "$aline\n";
+}
+close IN;
+
+print OUT "<p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution_after_count_filter.txt\"> length file</a>
+</p>
+";
+
+#### rfam
+unless ($rfampath=~/\/$/) {
+	$rfampath .="/";
+}
+unless ($genomepath=~/\/$/) {
+	$genomepath .="/";
+}
+print OUT "<h2>2. Rfam non-miRNA annotation</h2>
+<h3>2.1 Reads count</h3>
+<table border=\"1\">
+<tr align=\"center\">
+";
+
+my @rfamR; my @rfamT;
+my $tag=1;
+open IN,"<$dir/rfam_match/rfam_non-miRNA_annotation.txt";
+while (my $aline=<IN>) {
+	chomp $aline;
+	$tag=0 if($aline=~/tags\s+number/);
+	next if($aline=~/^\#/);
+	next if($aline=~/^\s*$/);
+	my @tmp=split/\s+/,$aline;
+	if($tag == 1){push @rfamR,[@tmp];}
+	else{push @rfamT,[@tmp];}
+}
+close IN;
+
+
+print OUT "<th>RNA Name</th>\n";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+for (my $i=0;$i<@rfamR;$i++) {
+	print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">$rfamR[$i][0]</th>
+	";
+	for (my $j=1;$j<@{$rfamR[$i]} ;$j++) {
+	print OUT "<td> $rfamR[$i][$j]</td>\n";
+	}
+}
+
+print OUT "</tr>\n</table>
+  <h3>2.2 Tags count</h3>
+  <table border=\"1\">
+   <tr align=\"center\">
+   <th>RNA Name</th>\n";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+for (my $i=0;$i<@rfamT;$i++) {
+	print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">$rfamT[$i][0]</th>
+	";
+	for (my $j=1;$j<@{$rfamT[$i]} ;$j++) {
+	print OUT "<td> $rfamT[$i][$j]</td>\n";
+	}
+}
+print OUT "</tr>\n</table>
+<p>Note:<br />The rfam mapping results is: <b>$rfampath</b>";
+print OUT "<b>rfam_mapped.bwt</b></p>";
+
+open IN,"<$dir/genome_match/genome_mapped.bwt";
+my @genome_r_u;
+my @genome_r_m;
+my @genome_t_u;
+my @genome_t_m;
+my $tags_map_number=0;
+while (my $aline=<IN>) {
+	chomp $aline;
+	my @temp=split/\t/,$aline;
+	if ($temp[6]==0) {
+		$aline=~/:([\d|_]+)_x(\d+)/;
+		my @lng=split/_/,$1;
+		for (my $i=0;$i<@lng;$i++) {
+			if ($lng[$i]>0) {
+				$genome_r_u[$i] +=$lng[$i];
+				$genome_t_u[$i] ++;
+			}
+		}
+		$tags_map_number++;
+	}
+	if ($temp[6]>0) {
+		$aline=~/:([\d|_]+)_x(\d+)/;
+		my @lng=split/_/,$1;
+		for (my $i=0;$i<@lng;$i++) {
+			if ($lng[$i]>0) {
+				$genome_r_m[$i] +=$lng[$i];
+				$genome_t_m[$i] ++;
+			}
+		}
+		for (my $i=0;$i<$temp[6] ;$i++) {
+			my $next=<IN>;
+		}
+		$tags_map_number++;
+	}
+}
+close IN;
+#<h3>3.1 Reads count</h3>
+#<table border=\"1\">
+#<tr align=\"center\">
+print OUT "<h2>3. genome mapping result</h2>
+<table border=\"1\">
+<tr align=\"center\">
+<th align=\"left\">Map</th>\n
+";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Uniq Map Reads No.</th>
+";
+for (my $i=0;$i<@genome_r_u ;$i++) {
+	print OUT "<td> $genome_r_u[$i]</td>\n";
+}
+
+print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Uniq Map Tags No.</th>
+";
+for (my $i=0;$i<@genome_t_u ;$i++) {
+	print OUT "<td> $genome_t_u[$i]</td>\n";
+}
+
+print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Multiple Map Reads No.</th>
+";
+for (my $i=0;$i<@genome_r_m ;$i++) {
+	print OUT "<td> $genome_r_m[$i]</td>\n";
+}
+
+print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Multiple Map Tags No.</th>
+";
+for (my $i=0;$i<@genome_t_m ;$i++) {
+	print OUT "<td> $genome_t_m[$i]</td>\n";
+}
+
+print OUT "</tr>\n</table>
+<p>Note:<br />The genome mapping results is: <b>$genomepath</b>";
+print OUT "<b>genome_mapped.bwt</b></p>";
+
+my $cluster="$clusterpath/sample_reads.cluster";
+my $cluster_number=`less $cluster |wc -l `;
+$cluster_number=$cluster_number-1;
+my (%cluster_length,@exp,@rpkm);
+my @exp_range=qw(0 \(0--10] \(10--100] \(100--1000] \(1000--10000] \(10000--100000] \(100000--**\));
+my @rpkm_range=qw(0 \(0--0.25] \(0.25--0.5] \(0.5--1] \(1.0-5.0] \(5--10] \(10--50] \(50--100] \(100--500] \(500--1000] \(1000--**]);
+
+open IN,"<$cluster";
+while (my $aline=<IN>) {
+	next if($aline=~/^\"/);
+	chomp $aline;
+	my @temp=split/\t/,$aline;
+	my @id=split/:|-/,$temp[0];
+	$cluster_length{$id[2]-$id[1]+1}++;
+	for (my $i=0;$i<@marks ;$i++) {
+		if ($temp[$i+3] == 0) {$exp[0][$i]++;}
+		elsif ($temp[$i+3]>0 && $temp[$i+3]<= 10  ){$exp[1][$i]++;}
+		elsif ($temp[$i+3]>10 && $temp[$i+3]<=100){$exp[2][$i]++;}
+		elsif ($temp[$i+3]>100 && $temp[$i+3]<=1000){$exp[3][$i]++;}
+		elsif ($temp[$i+3]>1000 && $temp[$i+3]<=10000){$exp[4][$i]++;}
+		elsif ($temp[$i+3]>10000 && $temp[$i+3]<=100000){$exp[5][$i]++;}
+		elsif ($temp[$i+3]>100000){$exp[6][$i]++;}
+	}
+}
+close IN;
+
+my $cluster_rpkm="$clusterpath/sample_rpkm.cluster";
+open IN,"<$cluster_rpkm";
+while (my $aline=<IN>) {
+	next if($aline=~/^\#/);
+	chomp $aline;
+	my @temp=split/\t/,$aline;
+	for (my $i=0;$i<@marks ;$i++) {
+		if ($temp[$i+3]==0) {$rpkm[0][$i]++;}
+		elsif($temp[$i+3]>0 && $temp[$i+3]<=0.25){$rpkm[1][$i]++;}
+		elsif($temp[$i+3]>0.25 && $temp[$i+3]<=0.5){$rpkm[2][$i]++;}
+		elsif($temp[$i+3]>0.5 && $temp[$i+3]<=1){$rpkm[3][$i]++;}
+		elsif($temp[$i+3]>1 && $temp[$i+3]<=5){$rpkm[4][$i]++;}
+		elsif($temp[$i+3]>5 && $temp[$i+3]<=10){$rpkm[5][$i]++;}
+		elsif($temp[$i+3]>10 && $temp[$i+3]<=50){$rpkm[6][$i]++;}
+		elsif($temp[$i+3]>50 && $temp[$i+3]<=100){$rpkm[7][$i]++;}
+		elsif($temp[$i+3]>100 && $temp[$i+3]<=500){$rpkm[8][$i]++;}
+		elsif($temp[$i+3]>500 && $temp[$i+3]<=1000){$rpkm[9][$i]++;}
+		else{$rpkm[10][$i]++;}
+	}
+}
+
+close IN;
+
+my $cluster_length_file="$clusterpath/cluster_length.txt";
+open LEN,">$cluster_length_file";
+print LEN "\#length\tcluster_number\n";
+foreach my $key (sort keys %cluster_length) {
+	print LEN "$key\t$cluster_length{$key}\n";
+}
+close LEN;
+print OUT "<h2>4. cluster result</h2>
+<h3>4.1 Cluster count</h3>
+<table border=\"1\">
+<tr align=\"center\">
+<th align=\"left\"> </th>
+<td>Merged samples</td></tr>
+<tr align=\"center\">
+<th align=\"left\">Tags number</th>
+<td>$tags_map_number</td></tr>
+<tr align=\"center\">
+<th align=\"left\">Cluster number</th>
+<td>$cluster_number</td></tr>\n</table>
+";
+
+print OUT "<h3>4.2 Cluster length</h3>
+<p> Note:<br />The clusters length data: <a href=\"./$clusterdir/cluster_length.txt\"> length file</a>
+</p>
+";
+print OUT "<h3>4.3 Quantify</h3>
+<table border=\"1\">
+<tr align=\"center\">
+<th align=\"left\">Reads Range</th>\n
+";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+for (my $i=0;$i<@exp_range;$i++) {
+	print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">$exp_range[$i]</th>
+	";
+	for (my $j=0;$j<@marks ;$j++) {
+		if (!(defined($exp[$i][$j]))) {
+			print OUT "<td> 0</td>\n";
+		}
+		else{print OUT "<td> $exp[$i][$j]</td>\n";}
+	}
+}
+print OUT "</tr>\n</table>";
+
+print OUT "\n<table border=\"1\">
+<tr align=\"center\">
+<th align=\"left\">RPKM Range</th>\n
+";
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+for (my $i=0;$i<@rpkm_range;$i++) {
+	print  OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">$rpkm_range[$i]</th>
+	";
+	for (my $j=0;$j<@marks ;$j++) {
+		if (!(defined($rpkm[$i][$j]))) {
+			print OUT "<td> 0</td>\n";
+		}
+		else{print OUT "<td> $rpkm[$i][$j]</td>\n";}
+	}
+}
+print OUT "</tr>\n</table>";
+
+my $annotate="$annotatepath/sample_c_p.anno";
+my (%posit,%repeat,%nat1,%nat2);
+my (@phase,@long,@repeat,@nat);
+for (my $j=0;$j<@marks ;$j++) {
+	$phase[$j]=0;
+	$long[$j]=0;
+	$repeat[$j]=0;
+	$nat[$j]=0;
+}
+
+my $class_anno=1;
+open ANNO,"<$annotate";
+while (my $aline=<ANNO>) {
+	chomp $aline;
+	my @temp=split/\t/,$aline;
+	if($aline=~/^\#/){
+		if (@temp != 10+@marks) {
+			$class_anno=0;
+		}
+		next;
+	}
+	for (my $i=3+@marks+$class_anno;$i<@temp;$i++) {
+		my @posit=split/\;/,$temp[$i];
+		for (my $j=0;$j<@marks ;$j++) {
+			if ($temp[3+$j]>0) {
+				$posit{$posit[0]}[$j]++;
+			}
+			else{
+				if (!(defined($posit{$posit[0]}[$j]))) {
+					$posit{$posit[0]}[$j]=0;
+				}
+			}
+		}
+	}
+	if ($class_anno) {
+		for (my $j=0;$j<@marks ;$j++) {
+			if ($temp[3+$j]>0) {
+				if ($temp[6] eq "phase") {
+					$phase[$j]++;
+				}
+				if ($temp[7] eq "long") {
+					$long[$j]++;
+				}
+				if ($temp[8] ne "\/") {
+					$repeat[$j]++;
+					my @rr=split/\;/,$temp[8];
+					foreach  (@rr) {
+						$repeat{$_}[$j]++;
+					}
+				}
+				if ($temp[9] ne "\/") {
+					$nat[$j]++;
+					my @nn1=split/\;/,$temp[9];
+					my @nn2=split/\;/,$temp[10];
+					for (my $k=0;$k<@nn1 ;$k++) {
+						$nat1{$nn1[$k]}[$j]++;
+						$nat2{$nn2[$k]}[$j]++;
+					}
+				}
+			}
+		}
+	}
+}
+close ANNO;
+
+print OUT "<h2>5. Cluster Annotate</h2>
+<h3>5.1 Cluster genome position annotate</h3>
+<table border=\"1\">
+<tr align=\"center\">
+<th align=\"left\">clusters number</th>\n
+";
+
+foreach  (@marks) {
+	print OUT "<th> $_ </th>\n";
+}
+foreach my $key (sort keys %posit) {
+	print  OUT "</tr>
+		<tr align=\"center\">
+		<th align=\"left\">$key</th>
+	";
+	foreach  (@{$posit{$key}}) {
+		print OUT "<td> $_</td>\n";
+	}
+}
+print OUT "</tr>\n</table>";
+print OUT "<p>
+Note:<br />
+One cluster mybe annotate to multiple genes<br />
+";
+
+if ($class_anno) {
+	print OUT "<h3>5.2 Cluster source mechanism annotate</h3>
+	<table border=\"1\">
+	<tr align=\"center\">
+	<th align=\"left\">clusters number</th>\n
+	";
+
+	foreach  (@marks) {
+		print OUT "<th> $_ </th>\n";
+	}
+	print OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Phase</th>\n
+	";
+	foreach  (@phase) {
+		print OUT "<td> $_ </td>\n";
+	}
+
+	print OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Long</th>\n
+	";
+	foreach  (@long) {
+		print OUT "<td> $_ </td>\n";
+	}
+
+	print OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Repeat</th>\n
+	";
+	foreach  (@repeat) {
+		print OUT "<td> $_ </td>\n";
+	}
+
+	print OUT "</tr>
+	<tr align=\"center\">
+	<th align=\"left\">Nat</th>\n
+	";
+	foreach  (@nat) {
+		print OUT "<td> $_ </td>\n";
+	}
+	print OUT "</tr>\n</table>";
+
+	print OUT "<p>
+	Repeat subclass annotate:
+	";
+
+	print OUT "<table border=\"1\">
+	<tr align=\"center\">
+	<th align=\"left\">Repeat subclass</th>\n
+	";
+	foreach  (@marks) {
+		print OUT "<th> $_ </th>\n";
+	}
+
+	foreach my $key (sort keys %repeat) {
+		print  OUT "</tr>
+			<tr align=\"center\">
+			<th align=\"left\">$key</th>
+		";
+		for (my $i=0;$i<@marks ;$i++) {
+			if (defined($repeat{$key}[$i])) {
+				print OUT "<td> $repeat{$key}[$i] </td>\n";
+			}
+			else{print OUT "<td> 0 </td>\n";}
+		}
+	}
+	print OUT "</tr>\n</table>";
+
+
+	print OUT "<p>
+	Nat subclass1 annotate:
+	";
+
+	print OUT "<table border=\"1\">
+	<tr align=\"center\">
+	<th align=\"left\">Nat subclass1</th>\n
+	";
+	foreach  (@marks) {
+		print OUT "<th> $_ </th>\n";
+	}
+	foreach my $key (sort keys %nat1) {
+		print  OUT "</tr>
+			<tr align=\"center\">
+			<th align=\"left\">$key</th>
+		";
+		for (my $i=0;$i<@marks ;$i++) {
+			if (defined($nat1{$key}[$i])) {
+				print OUT "<td> $nat1{$key}[$i] </td>\n";
+			}
+			else{print OUT "<td> 0 </td>\n";}
+		}
+	}
+	print OUT "</tr>\n</table>";
+
+	print OUT "<p>
+	Nat subclass2 annotate:
+	";
+
+	print OUT "<table border=\"1\">
+	<tr align=\"center\">
+	<th align=\"left\">Nat subclass2</th>\n
+	";
+	foreach  (@marks) {
+		print OUT "<th> $_ </th>\n";
+	}
+	foreach my $key (sort keys %nat2) {
+		print  OUT "</tr>
+			<tr align=\"center\">
+			<th align=\"left\">$key</th>
+		";
+		for (my $i=0;$i<@marks ;$i++) {
+			if (defined($nat2{$key}[$i])) {
+				print OUT "<td> $nat2{$key}[$i] </td>\n";
+			}
+			else{print OUT "<td> 0 </td>\n";}
+		}
+	}
+	print OUT "</tr>\n</table>";
+	print OUT "<p>
+	Note:<br />
+	One cluster mybe annotate to multiple repeats or nats<br />
+	";
+}
+else {
+	print OUT "<h3>5.2 Cluster source mechanism annotate</h3>
+	<br />Do not do source mechanism annotate <br />";
+
+}
+
+print OUT "<h2>6. Graph of Clusters of all samples</h2> \n";
+
+my $plot=$plotpath."cluster.html";
+open IN,"<$plot";
+while (my $aline=<IN>) {
+	chomp $aline;
+	print OUT "$aline\n";
+}
+close IN;
+
+
+if ($deg_tag) {
+	my $deg_file=`ls $degpath`;
+	chomp $deg_file;
+	my @deg_file=split/\n/,$deg_file;
+	my %deg;
+	foreach  (@deg_file) {
+		my $output="$degpath/$_/output_score.txt";
+		open IN,"<$output";
+		$deg{$_}[0]=0;
+		$deg{$_}[1]=0;
+		$deg{$_}[2]=0;
+		while (my $aline=<IN>) {
+			next if ($aline=~/^\"/);
+			chomp $aline;
+			my @temp=split/\t/,$aline;
+			if ($temp[9] eq "TRUE") {
+				$deg{$_}[0]++;
+				if ($temp[4] >0) {
+					$deg{$_}[1]++;
+				}
+				if ($temp[4] <0) {
+					$deg{$_}[2]++;
+				}
+			}
+		}
+		close IN;
+	}
+
+	print OUT "<h2>7. DEG</h2>
+	<table border=\"1\">
+	<tr align=\"center\">
+	<th align=\"left\">Genes number</th>\n
+	<th> DEG </th>\n
+	<th> UP </th>\n
+	<th> DOWN </th>\n
+	";
+
+	foreach my $key (sort keys %deg) {
+		print  OUT "</tr>
+			<tr align=\"center\">
+			<th align=\"left\">$key</th>
+		";
+		for (my $i=0;$i<@{$deg{$key}} ;$i++) {
+			print OUT "<td> $deg{$key}[$i] </td>\n";
+		}
+	}
+	print OUT "</tr>\n</table>";
+}
+else{
+	print OUT "<h2>7. DEG</h2>
+	<br />Do not do DE clusters <br />";
+}
+
+print OUT "
+ </BODY>
+</HTML>
+";
+close OUT;
+
+
+
+
+sub usage{
+print <<"USAGE";
+Version $version
+Usage:
+$0 -o
+options:
+-i 
+-format
+-o output file
+-h help
+USAGE
+exit(1);
+}