Hello perlmonks,
I am writing a program that checks a directory for FASTA (.fa) files (containing DNA sequences), opens them and prints out the names of the corresponding sequencing (characterised by '>' at the beginning of a line). However, my code cannot open the files and I don't know what the problem is.
Here's my code: 

my $dir = "directory/";
opendir ( DH, $dir ) || die "Cannot open $dir: $!.\n";
foreach ( readdir DH) {
    if (/\.fa$/){
        my $file = $_;
        open (READ, "$file") || die "Cannot open $file: $!.\n";  # her
+e's the problem
        while (<READ>){
            if ( /^>/){
                print $_;
            }
        } 
    } close (READ);
} close (DH);

[download]

I could of course store each file name in a variable and open the files outside the loop, but I prefer a one-pass solution. Any ideas?

In reply to Cannot open file within a loop by ic23oluk

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