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author bigrna
date Sun, 04 Jan 2015 02:47:25 -0500
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#!/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);
}