The code below does really what I want it to do, but it also adds extra information that I don't want.

The batch file consists of a list of batches that have been run and I need this list to look at folders that have this name.

The list file is a list of samples that I need to get the information from in report files.

The report files is a list of tab delimited results where I need to get the third and 23rd tab. From the first report file I need all the samples that are in the list file. From the second report file I only need the sample that I don’t have already. I know it can be done by using an exist, but I can’t get my head around how it should look like.

Thanks for your help.

#!/usr/bin/perl -w

=head
 Title    : apt_SNPCall_report
 Function : To combine the results from the different reports based on
+ the batch list.
=cut
#---------------------------------------------------------------------
+----------
# use and library files
use strict;
use Getopt::Long;

#---------------------------------------------------------------------
+----------
# Get options
my ($help, $batch, $list);
my $output = "genotyping_results.txt";
my ($good_batch, $out_name, $out_dir_name);
my (@list_files, %sample);


sub help {
  print <<EOH;

Description:
Using the apt_SNP_batch_call will generate reports for each of the sep
+arate samples that failed QC together with either samples that passed
+ QC or HapMap reference samples. This script will combine the results
+ from each of the report files into one table containing the SNP call
+ rate and the pm_mean (average intensity).

Input files
The script will search for the customer samples using

Known issues/bug/beware...
NA

Use:
  perl $0 [options]

Options and arguments:
-help              this
--batch            Name of the file that contains the batches used for
+ genotyping       [mandatory]
--list             File containing the list of CEL files of interest  
+                  [mandatory]
--output           Name of output file                                
+                  [optional]

EOH
  $help  =  1;
  exit;
}

#---------------------------------------------------------------------
+----------
# Options:
GetOptions(
           'help'      => \$help,
       'batch=s'   => \$batch,
       'list=s'    => \$list,
       'output=s'  => \$output
           );
if ((! $batch) or (! $list) or $help){ 
  &help();
}

# File opening:
open (BATCH, $batch) || die "Cannot open input file $batch: $!\n";
open (LIST, $list) || die "Cannot open input file $list: $!\n";
open (W, ">$output") || die "Error to open $!";

#---------------------------------------------------------------------
+----------
# Script

#print W "SampleName\tcall_rate\tpm_mean\n";
print "SampleName\tcall_rate\tpm_mean\n";

while (<LIST>) {
    chomp;
    my ($path, $file) = ($_ =~ /(.*\/)(.*)/);
    push (@list_files, $file);
}
close LIST;

while (<BATCH>) {
    chomp;
    s/\r//;
    my $filename = $_;
    $out_name = $filename;
    $out_name =~ s/\.txt//;
    $out_dir_name = "apt_SNPCall_".$out_name;
    foreach my $lf (@list_files){
    open (SAMPLE, "$out_dir_name/birdseed-v2.report.txt") || die "Erro
+r to open: $!";
    while (<SAMPLE>) {
        chomp;
        my @tab = split("\t", $_);
        if ($tab[0] eq $lf){
        my $sample = $lf;
        $sample =~ s/\.CEL//;
        print $sample."\t".$tab[2]."\t".$tab[22]."\n"; #I get problems
+ here
#        print W $sample."\t".$tab[2]."\t".$tab[22]."\n";
        }

    }
    }
}

close SAMPLE;
close W;
close BATCH;

###################################
# Functions
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