annotate quantify.pl @ 33:09fefe8db1d0 draft default tip

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#!/usr/bin/perl -w
#Filename:
#Author: chentt
#Email:
#Date: 2012-4-6
#Modified:
#Description:
my $version=1.00;

use strict;
use Getopt::Long;

my %opts;
GetOptions(\%opts,"i=s","o=s","d=s","h");
if (!(defined $opts{i} and defined $opts{d} and defined $opts{o}) || defined $opts{h}) { #necessary arguments
&usage;
}

my $input=$opts{'i'};
my $output=$opts{'o'};
my $depth=$opts{'d'};

open (IN,"<$input")||die"$!";
open OUT,">$output";
#my @Total=qw(15797079 18042650 17455254 17295526 18791753 16719596 15150009 18451484 17402501 17729362 19347595 17518516 15699663 16589265 15442892 14012264 14190746 17280260 13213117 12390121 14874304 );
my @Total=split/\,/,$depth;
#print OUT "#clusterID\tmajor_length\tpercent\n";
while (my $aline=<IN>) {
	chomp $aline;
	if ($aline=~/^\"/){
		my @title=split/\t/,$aline;
		for (my $i=0;$i<@title ;$i++) {
			$title[$i]=~s/^\"(\S+)\"$/$1/;
		}
		my $title=join "\t",@title;
		print OUT "\#$title\n";
		next;
	}
	my @temp=split/\t/,$aline;
	print OUT "$temp[0]\t$temp[1]\t$temp[2]";
	my @id=split/:/,$temp[0];
	my @posi=split/-/,$id[1];
	for (my $i=3;$i<@temp;$i++) {
		my $rpkm=sprintf("%.2f",$temp[$i]/($posi[1]-$posi[0]+1)/$Total[$i-3]*1000000000);
		print OUT "\t$rpkm";
	}
	print OUT "\n";
}
close IN;
close OUT;

sub usage{
print <<"USAGE";
Version $version
Usage:
$0 -i -o -h
options:
-i input cluster file
-o output file
-d depth
-h help
USAGE
exit(1);
}