use strict;
use warnings;

my $i=0;
sub matrix {
  my ( $filepath ) = @_;

  # new array
  my @values;

  # open file for reading
  open my $fh, '<', $filepath or die "$filepath: open failed: $!\n";

  my $i = 0;
  while ( my $line = <$fh> ) {
    $i++;
    # skip commented lines
    next if $line =~ m{^#};

    # remove line breaks; obsolete because of following s/\s+//g
    # but good idea to do this (what happens if the s///g is gone?) ;o)
    chomp $line;

    # remove any white spaces (including line breaks)
    $line =~ s/\s+//g;

    push @values, [ split m{,}, $line ];
  }
  
  close $fh or die "$filepath: close failed: $!\n";

  # return number of read lines and reference to this array
  return $i, \@values;
}

my ( $count, $array_r ) = matrix( '/path/to/file' );