comment on

Some comments:

I prefer to almost always use a defined "my $variable" in a loop, especially when using nested loops each of which use $_. Doing otherwise can lead to problems. Using a "my" variable instead of $_ is very "cheap" execution time wise.
Normally assigning $_ to a variable is not needed. Do that as part of the loop setup.
In the "die" message, a trailing "\n" will suppress the Perl line number upon which the error occurred. For code like this, normally you will want a direct reference to the line number where the open failed, so don't put a trailing "\n". In some user programs, maybe the actual line number is confusing and you want a \n to suppress that. In any event, be aware of this difference.
Normally do not put a trailing "/" at the end of the directory name. This can at least confuse Windows on occasion. Prepend a "/" when expanding the path, "$dir/$sub_dir/$file".
Of course, readdir() returns just a name, not the full path, so that needs to be corrected in the open().

I think this should work, (untested):

my $dir = "directory";  #### no trailing "/"
opendir ( DH, $dir ) || die "Cannot open $dir: $!"; #### no "\n"

foreach my $file ( readdir DH) # Note: only name, not full path
{
   next unless $file =~ /\.fa$/;
   
   open (READ, '<', "$dir/$file") || die "Cannot open $dir/$file: $!";
+  

   while (my $line =<READ>)
   {
      if ($line =~ /^>/)
      {
         print $line;
      }
   } 
   close READ;   
} 

close (DH);
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In reply to Re: Cannot open file within a loop by Marshall
in thread Cannot open file within a loop by ic23oluk

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