I can't see how that's possible. The only thing you append to the file is a newline.
Here's a guess on what you're really looking for. You want to append the three files to the $fa file. You'll need to open each in turn, read from it, then print the contents to the $fa file (those variable names could really be more descriptive, by the way).
So I think what you want is something like this:
#!/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 na
+me
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 $f
+a
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);
}
}
}
}
}
}
Note that this is a very quick revision of your code, with added error checks (and just noticed I missed the readdir, doh). And it may not be at all what you want. If not, please provide more detail on what you're trying to do.
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