I think you want something like this (untested):

my $dir = 'C:/Documents and Settings/mydir/Desktop/current/Test_Files'
+;
open my $out, '>', "$dir/data.txt" or die "can't open out file: $!";
opendir my $dh, $dir or die "can't opendir $dir : $!";
while(my $f = readdir($dh)) {
  next if ($f eq 'data.txt');
  open my $fh, '<', "$dir/$f" or die "can't open file $f : $!";
  my $first_line = <$fh>;
  while (my $line = <$fh>) {
    chomp $line;
    my ($well,$sample,$barcode,$block_id) = split(/\t/, $line);
    my $name = substr($block_id, 11);
    $sample =~ /(\d+)(.*)/;
    print $outfile "$well\t$1\t$2\$barcode\t$name\n";
  }
  close $fh;
}
closedir $dh;
close $out;
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Notes:

• readdir lets you loop over all the files in a directory, but you still need to open and read each file.
• It's not good to write your output into the same place all your input files are - your script will try to read it too!
• Be careful using the special variable $_ - this is the "default" output of many operations, so it's easy for one to clobber another. I like to store lines read from a file into a variable, just to be safe.
• The special variables $1 and $2 (regex matches) are also easy to clobber (what if you add another regex to your script sometime in the future?) So either store them in other variables right after the regex, or else use them immediately.

You pointed me in the right direction! The script works even
though I get that annoying "use of uninitialized value of $1 and $2
in concatenation(.) or string at my print $out statement line.
Should I be concerned about that?


my $dir = 'C:/Documents and Settings/mydir/Desktop/current/Test_Files'
+;
# directory to search
opendir my $dh, "$dir"; 
my $i=1;
while(my $f = readdir($dh)) {
    next if -d "$dir/$f";
    open(my $in, "$dir/$f");
    open(my $out,  ">C:/Documents and Settings/mydir/Desktop/current/T
+est_Files/outfiles/data$i");
    my $firstline = <$in>;
    chomp $firstline;
    while(my $line = <$in>){
        chomp $line;
        my ($well_position,$sample,$barcode,$block_id) = split(/\t/, $
+line);
        my $name = substr($block_id, 11);
        $sample =~ /(\d+)(.*)|(\D\d))/;
        print $out "$well_position\t$1\t$2\t$barcode\t$name\n";
    }
    $i++;
    close($in);
    close($out);
}
closedir($dh);
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Thanks!
LomSpace

I get that annoying "use of uninitialized value of $1 and $2 in concatenation(.) or string at my print $out statement line. Should I be concerned about that?

If you are asking this question, that means there is something that you do not understand about your code. Yes, you should be concerned, and yes, you should try to determine the root cause of the warning.

As an aside, you should always check the results of each open and opendir:

opendir my $dh, $dir or "Can not open directory $dir: $!";
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I'll bet you have lines in your data files that don't match the regex, so the $1 and $2 values are undefined, then you try to use them in the print statement. One solution is to simply cleanup the input files before running the script (i.e., make sure there are no files in the input directory other than files you want the script to process). The other possibility is that your data has junk in it - maybe blank lines or comment lines? If so, you simply need to check for those and skip them as needed.

while(my $line = <$in>) {
  chomp $line;
  $line =~ s/^\s+//;      # strip leading whitespace
  next unless $line;      # skip blank lines
  next if ($line =~ /^#/; # skip comment line

  ...

}
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Another thing you can do is this:

my ($x, $y) = $sample =~ /(\d+)(.*)/;
$x = '?' unless $x;
$y = '?' unless $y;
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This saves the regex matches into variables, so you don't have to use the special vars $1 and $2 anymore, and you can test them, give them default values, etc.

while(my $f = readdir($dh)){
   next if -d "$dir/$f";
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That is a good look Toolic!
Thanks!
LomSpace

$sample = $fields[1];
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This is not clear, particularly '$_'. I can process using open, but I run into
problems with opendir and readdir. I want to change the format of the files.
Read more... (970 Bytes)
Still stuck }

try the following on the command line

perl -e 'opendir DIR, "./";@directory =readdir(DIR);for $entry (@direc
+tory){print "$entry\n";}'
[download]

in your while loop in the failing example $f is a string with the name of a file in it, you have to open, process and close the file inside the loop