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diff html_preprocess.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_preprocess.pl	Sun Jan 04 02:47:25 2015 -0500
@@ -0,0 +1,388 @@
+#!/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","min=i","max=i","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,$knownpath,$genomepath,$novelpath);
+my ($predir,$rfamdir,$knowndir,$genomedir,$noveldir);
+open IN,"<$opts{i}";
+$config=<IN>; chomp $config;
+$prepath=<IN>; chomp $prepath;
+$genomepath=<IN>; chomp $genomepath;
+$rfampath=<IN>;
+close IN;
+my @tmp=split/\//,$prepath;
+$predir=$tmp[-1];
+@tmp=split/\//,$genomepath;
+$genomedir=$tmp[-1];
+
+my $dir=dirname($opts{'o'});
+
+open OUT ,">$opts{'o'}";
+print OUT "<HTML>\n  <HEAD>\n  <TITLE> Analysis Report </TITLE>\n </HEAD>
+ <BODY bgcolor=\"lightgray\">\n  <h1 align=\"center\">\n    <font face=\"ºÚÌå\">\n	<b>Preprocess Report</b>\n  </font>\n  </h1>
+  <h2>1. Sequence No. and quality</h2>
+  <h3>1.1 Sequece No.</h3>
+";
+
+### raw data no
+open IN,"<$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_$opts{min}_$opts{max}.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;
+
+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> $_ </td>\n";
+}
+print OUT "</tr>\n</table>";
+print OUT "<p>
+Note:<br />
+The raw data file path is: <b>$files[0]</b><br />
+";
+for (my $i=1;$i<@files;$i++) {
+	print OUT "&nbsp;&nbsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;<b>$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 />
+</p>
+<h2> 1. Sequence length count</h2>
+<h3> 1.1 Reads length count </h3>
+";
+print OUT "\n";
+
+my (%length); my $key="Tags Length";
+open IN,"<$prepath/reads_length_distribution.txt";
+while (my $aline=<IN>) {
+	chomp $aline;
+	next if($aline=~/^\s*$/);
+	if ($aline=~/^Reads/) { $key="Reads Length";}
+	my @tmp=split/\t/,$aline;
+	my @array=split/\s/,$tmp[1];
+	push @{$length{$key}},[$tmp[0],@array];
+}
+close IN;
+
+print OUT "<table border=\"1\">
+<tr align=\"center\">";
+my $hashkey="Reads Length";
+foreach  (@{$length{$hashkey}[0]}) {
+	print OUT "<th> $_ </th>\n";
+}
+print  OUT "</tr>";
+
+for (my $i=1;$i<@{$length{$hashkey}};$i++) {
+	print OUT "<tr align=\"center\">
+	<th >$length{$hashkey}[$i][0] </th>
+	";
+	for(my $j=1;$j<@{$length{$hashkey}[$i]};$j++) {
+		print OUT "<td> $length{$hashkey}[$i][$j] </td>\n";
+	}
+	print OUT "</tr>\n";
+}
+print OUT "</table>\n";
+
+print OUT "<h3> 1.2 Tags length count </h3>";
+
+print OUT "<table border=\"1\">
+<tr align=\"center\">";
+$hashkey="Tags Length";
+foreach  (@{$length{$hashkey}[0]}) {
+	print OUT "<th> $_ </th>\n";
+}
+print  OUT "</tr>";
+
+for (my $i=1;$i<@{$length{$hashkey}};$i++) {
+	print OUT "<tr align=\"center\">
+	<th > $length{$hashkey}[$i][0] </th>
+	";
+	for(my $j=1;$j<@{$length{$hashkey}[$i]};$j++) {
+		print OUT "<td> $length{$hashkey}[$i][$j] </td>\n";
+	}
+	print OUT "</tr>\n";
+}
+
+print OUT "</table>\n";
+
+print OUT "<h2> 2. Sequence length distribution </h2>";
+my $length=$prepath."length.html";
+open IN,"<$length";
+while (my $aline=<IN>) {
+	chomp $aline;
+	print OUT "$aline\n";
+}
+
+#print OUT "<p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution.txt\"> length file</a>
+#</p>
+#";
+
+
+
+
+####genome map
+#unless ($genomedir=~/\/$/) {
+#	$genomedir .="/";
+#}
+
+print OUT "<h2>2. Genome Alignment Result</h2>
+<h3>2.1 Mapping count</h3>
+";
+
+open IN,"<$genomepath/genome_mapped.fa";
+my (@gread,@gtag);
+while (my $aline=<IN>) {
+	chomp $aline;
+	<IN>;
+	$aline=~/:([\d|_]+)_x(\d+)$/;
+	my @sss=split/_/,$1;
+	for (my $i=0;$i<@sss;$i++) {
+		if ($sss[$i]>0) {
+			$gread[$i] +=$sss[$i];
+			$gtag[$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\">Genome Mapped Reads No. </th>
+";
+foreach  (@gread) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Genome Mapped Reads Percent </th>
+";
+
+for (my $i=0;$i<@gread;$i++) {
+	my $per=sprintf ("%.2f",$gread[$i]/$cleanR[$i]*100);
+	print OUT "<td> $per\%</td>\n";
+}
+
+print  OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Genome Mapped Tags No. </th>
+";
+foreach  (@gtag) {
+	print OUT "<td> $_ </td>\n";
+}
+print OUT "</tr>
+<tr align=\"center\">
+<th align=\"left\">Genome Mapped Tags Percent </th>
+";
+
+for (my $i=0;$i<@gtag;$i++) {
+	my $per=sprintf ("%.2f",$gtag[$i]/$cleanT[$i]*100);
+	print OUT "<td> $per\%</td>\n";
+}
+print OUT "</tr>\n</table>";
+print OUT "<p>
+Note:<br />
+The genome mapped bwt file path is: <b>$genomedir/genome_mapped.bwt</b><br />
+The genome mapped FASTA file path is: <b>$genomedir/genome_mapped.fa</b>
+<br />
+";
+
+
+
+#### rfam
+if(defined $rfampath && $rfampath=~/rfam_match/){
+chomp $rfampath;
+@tmp=split/\//,$rfampath;
+$rfamdir=$tmp[-1];
+
+unless ($rfampath=~/\/$/) {
+	$rfampath .="/";
+}
+print OUT "<h2>3. Rfam non-miRNA annotation</h2>
+<h3>3.1 Reads count</h3>
+<table border=\"1\">
+<tr align=\"center\">
+";
+
+my @rfamR; my @rfamT;
+my $tag=1;
+open IN,"<$dir/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>3.2 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>
+";
+}
+
+
+print OUT "
+ </BODY>
+</HTML>
+";
+close OUT;
+
+sub usage{
+print <<"USAGE";
+Version $version
+Usage:
+$0 -o
+options:
+-o output file
+-h help
+USAGE
+exit(1);
+}
+