VALUE:while($file[$j][$n] =~ /\b\.+\b/gi)            # while there is still a digit there (i.e. not a name       
 
##</code><code>##

my @file;
push @{$file[0]}, 
  qw (YAL038W 1.1 2.4 4.1 YCL040W 99.2 1.1 1.6 1.8 9.11 0.040212811);
push @{$file[1]}, 
  qw(YDR223W 99 4.7 0.0085523710);
push @{$file[2]}, 
  qw(YDL188C 1.5.4 10.3.1 13.32 YGL134W 01.05.04 02.19 0.083130297);
$rows = 3;
my %seen;
@pathway_name = (1, 2, 4, 99); 


##</code><code>##

       VALUE:while($file[$j][$n] =~ /^[\.\d ]+$/) 

##</code><code>##

Pathway is 1
Gene: YAL038W, Value: 1.1 printed to output file
Gene: YDL188C, Value: 1.5.4 printed to output file
Pathway is 2
Gene: YAL038W, Value: 2.4 printed to output file
Pathway is 4
Gene: YAL038W, Value: 4.1 printed to output file
Gene: YDR223W, Value: 4.7 printed to output file
Pathway is 99