for($m = 0; $m < scalar(@pathway_name); $m++)  # foreach pathway name given by an integer
{
  print "Pathway is $pathway_name[$m]\n";      # e.g.pathway name is 1
 
  for($j = 0; $j < $rows; $j++)                # for each row in my 2-D converted input file $file[][]
  {
    $n = 1;
    #print "Gene: $file[$j][0], Value: $file[$j][1]\n";
    if($seen{$file[$j][0]})                               # if the indexing element has already been seen    
    {
      #print "Seen this Gene: $file[$j][0]\n";            # go on to the next row
    }
    elsif($file[$j][1])                                   # if the value exists
    {
      $n = 1;
      VALUE:while($file[$j][$n] =~ /\b\.+\b/gi)            # while there is still a digit there (i.e. not a name       
      {
        #print "Gene: $file[$j][0], Value:$file[$j][$n]\n";
        #print "Entering if statement in while block...\n";
 
        if($file[$j][$n] =~ /\b\Q$pathway_name[$m]\E\.\d+/)      # if matches the combination of pathwayname.digit.digit
        {
          print OUTPUT "$file[$j][0]\t$pathway_name[$m]\n";
          print "Gene: $file[$j][0], Value: $file[$j][$n] printed to output file\n";
          #print "Going to last value.\n";
          $seen{$file[$j][0]} = 1;                               # add the gene to the %seen hash for this pathway          
          last VALUE;
        }
        else
        {
          #print "Gene: $file[$j][0], Value: $file[$j][$n] not matched.\n";
          $n++;                                                   # go on to the next value
        }
      }                                                           # end while
    }                                                             # end elsif
    else
    {
     print "Skipped gene $file[$j][0]\n";                          # go on to the next line
    }
  }                                                              # end while ($j < $row)
undef %seen;                                                   # since going on to the next pathway, undefine %seen
}