sat_extract

#!/usr/bin/perl -w

use strict;
use FileHandle;
use File::Basename;
use Getopt::Long;

my @tmpline;
my $stock = "";
my $nseq = 1;
my $biggest = 0;
my $pflag = 0;
my $paired = 0;

my ($FILE,$OUTPUT_DIR) = ("duplicates_data.csv","./");

my $result = &GetOptions(
			 'f=s'       => \$FILE,
			 "o=s"       => \$OUTPUT_DIR
                        );
                        
opendir (DIR, $OUTPUT_DIR) or die $!;	
while (my $file = readdir(DIR)) {
	if ($file =~ /duplicates_reads_(.*).stats/){
		open(FILE,"<","$OUTPUT_DIR/$file");
		$stock .= int($1);
		$pflag = 0;
		while(<FILE>){
			@tmpline = split(" ",$_);
			if (@tmpline && ($tmpline[0] eq "nbReadsInSample=")){
				$stock .= "\t".$tmpline[$#tmpline];
				$pflag++;
			}
			if(@tmpline && $tmpline[0] eq "nbReadsInInput="){
				$nseq = $tmpline[1];
				if($biggest<$nseq){
					$biggest = $nseq;
				}
			}
		}
		if($pflag >= 3){
			$paired = 1;
		}
		$stock .= "\t".$nseq;
		$stock .= "\n";	
		close(FILE);

	}
}
closedir(DIR);
open(FTAB, ">", "$OUTPUT_DIR/$FILE");
if($paired==1){
	print FTAB "$biggest\tPAIRS\tREAD1\tREAD2\tNSEQ\n";
}else{
	print FTAB "$biggest\tDUPL\tNSEQ\n";
}
print FTAB $stock;
close(FTAB);