Hello
I am processing a lot of files in a directory. I tested the parsing
and it works fine. 
open(my $out, ">C:/Documents and Settings/mydir/Desktop/ltvec_data.txt
+");
my $first_line = <DATA>;
chomp $first_line;

while(<DATA>){
    chomp;
    my @fields = split /\t/;
    my $well_position = $fields[0];
    my $sample = $fields[1];
    $sample =~ /(\d+)(.*)/;
    my $barcode = $fields[2];
    my $block_id = $fields[3];
    my $name = substr($block_id,11);
    print $out "$well_position\t$1\t$2\t$barcode\t$name\n";
}
close $out;

__DATA__
Position    Sample    Barcode    
A01    12032 B1    NUBI825632    XXXXX Glyc 01/07/2009
B01    12032 L1    NUBI825757    XXXXX Glyc 01/07/2009
C01    12032 L2    NUBI825872    XXXXX Glyc 01/07/2009
D01    12032 L3    NUBI825997    XXXXX Glyc 01/07/2009
E01    12166 B1    NUBI826118    XXXXX Glyc 01/07/2009

[download]

This works fine. I have to perform the same parsing on 20+ files in a dir.
I revised the code to process the files files.
my $_dir = 'C:/Documents and Settings/mydir/Desktop/current/Test_Files
+';
open(my $out, ">C:/Documents and Settings/mydir/Desktop/current/Test_F
+iles/data.txt");
opendir my $dh, "$dir"; # read files in dir
#my $first_line = <IN>;
#chomp $first_line;
#my $i=1;
while(my $f = readdir($dh)){
    chomp;
    my @fields = split /\t/;
    my $well_position = $fields[0];
    my $sample = $fields[1];
    $sample =~ /(\d+)(.*)/;
    my $barcode = $fields[2];
    my $block_id = $fields[3];
    my $name = substr($block_id,11);
    my $outfile = "$out$name";
    print $outfile "$well_position\t$1\t$2\t$barcode\t$name\n";
}
closedir($dh);
</readmore>

[download]

I am getting several errors that are basically telling me that I using uninitialized variables($sample, $name, $_ in scalar chomp and split).
Any clues?

In reply to processing a lot of files by lomSpace

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