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

my @file;
push @{$file[0]}, 
...
my %seen;
@pathway_name = (1, 2, 4, 99);

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

Pathway is 1
Gene: YAL038W, Value: 1.1 printed to output file
...
Gene: YAL038W, Value: 4.1 printed to output file
Gene: YDR223W, Value: 4.7 printed to output file
Pathway is 99