#!/usr/bin/perl
use strict;
use Data::Dumper;
use File::Glob ':glob';
	
my @dirs = glob("C:/Documents and Settings/mydir/Desktop/KOMP/*");
foreach my $maid_dir(@dirs){
	if (-d $maid_dir){ # directory check
		if ($maid_dir=~m%\d+\s[A-Z]%){ # match the dir name
			my $seq_dir = $maid_dir."/sequencing/";
			chdir ($maid_dir);
			#next if (-M $seq_dir > 1.0);
			chdir ($seq_dir);
			#print Dumper ($maid_dir, $seq_dir);
			opendir my $dh, "$seq_dir";
			if(-d $seq_dir){
				my @files = readdir $dh;
				for my $f(@files){
					if($f=~ m%^(\d*)(HU.fa|HD.fa|Ltvec_small.FA|_fasta)$%){
						my ($fa, $hu, $hd, $lt)= ($1."_fasta", $1."HU.fa", $1."HD.fa", $1."Ltvec_small.FA");
						if(-e $fa){
							open (my $out, ">>".$seq_dir."/".$fa) or die "Can't open $seq_dir/$fa for append: $!\n";
							# Append the contents of the three files to $fa
							open my $hu_file, '<', $hu or die "Can't open $hu: $!\n";
							while (my $line = <$hu_file>) {
								print $out $line;
							}
							open my $hd_file, '<', $hd or die "Can't open $hd: $!\n";
							while (my $line = <$hd_file>) {
								print $out $line;
							}
							open my $lt_file, '<', $lt or die "Can't open $lt: $!\n";
							while (my $line = <$lt_file>) {
								print $out $line;
							}
							print $out, "\n";
							#print Dumper($f);
							close($out);
							close($hu_file);
							close($hd_file);
							close($lt_file);
						}
					}
				}			
			}		
		}	
	}	
}