#!/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) {
    # Combined the first two conditionals to reduce indentation
    if (-d $maid_dir and $maid_dir=~m%\d+\s[A-Z]%){ # match the dir name
        my $seq_dir = $maid_dir."/sequencing/";
        chdir ($maid_dir) or die "Can't chdir to $maid_dir: $!\n";
        next if (-M $seq_dir > 1.0);
        chdir ($seq_dir) or die "Can't chdir to $seq_dir: $!\n";
        #print Dumper ($maid_dir, $seq_dir);
        opendir my $dh, "$seq_dir" or die "Can't open $seq_dir: $!\n";
        if(-d $seq_dir){
            my @files = readdir $dh;
            #my $path = @_;
            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){
                        # This is output, not input. Renamed variable accordingly.
                        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;
                        }


                        #open( my $out, ">>".$seq_dir."/".$fa);
                        print $out, "\n" ;#"$hu,$hd,$lt\n";
                        print Dumper($f);
                        close($out);
                        close($hu_file);
                        close($hd_file);
                        close($lt_file);
                    }
                }
            }
        }
    }
}