Allo,

I've been going crazy with a program I'm writing using the BioPerl library. Problem could be my code, or the public data, or the library. I want to rule out myself before looking at others. I do not want anyone to go learn the library to help with this, just to see if I am doing something syntax incorrect of some sort.

I have not yet found a "minimal test-case" because each run of program on just two chromosomes is 6 hours on my PC! I removed most "excess" already though.

# includes
use strict;
use Bio::ClusterIO;

# locals
my $dir    = $ARGV[0];
my %data;

# directory handling
if (-d !$dir) {
    print    "Directory does not exist!\n",
        "Program Terminating....\n";
    exit();
    }
opendir(DIR, $dir) || die "$dir: $!\n";
chdir($dir);
$dir =~ s/\\$//;

while (my $infile = readdir(DIR)) {

    if ((-T $infile) && ($infile =~ /^ds_ch(.{1,2})\.xml$/i)) {

        my %data;
        my $chromosome = $1;

        print "Processing $chromosome\n";

        my $parser = Bio::ClusterIO->new(
                        -file    =>    $infile,
                        -format    =>    'dbSNP'
                        );

        while (my $record = $parser->next_cluster()) {

            if (my $class = $record->functional_class) {
                $class =~ s/^\s+//;
                $class =~ s/\s+$//;
                $data{$class}{$record->observed()}++;
                }
            }

        open(OUT, '>>', 'Results.txt');

        foreach my $class (keys(%data)) {
            foreach my $snp (keys(%{$data{$class}})) {
                print OUT "$chromosome\t$class\t$snp\t$data{$class}{$s
+np}\n";
                }
            }

        close(OUT);
        }

    }
[download]

Problem is: even if directory of 20 files is processed, file only contains output from one file, or sometimes none? Tried subsets of data-files (each 1GB) but no differences so far. Any help please!

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