Ah, indeed. That would have been the smart thing.
Righto.

For the data given:

YAL038W 1.1 2.4 4.1 YCL040W 1.1 1.6 1.8 9.11 0.040212811
YDR132C 99 YDR223W 99 0.0085523710
YDL188C 1.5.4 10.3.1 13.32 YGL134W 01.05.04 02.19 -0.083130297
[download]

and the variables:
@pathway_name = (1, 2, 4, 99); # looking for values starting with these numbers

Output:

<b>To command line</b>
Pathway is 1
Gene: YAL038W, Value: 1
Gene: YDL188C, Value: 1
Pathway is 2
Pathway is 4
Gene:YAL038W, Value: 4.1
Pathway is 99
Done.
<b>And in the file OUTPUT:</b>
YAL038W 1
YDL188C 1
YAL038W 4
[download]

It completely bypasses the 2 and 99 ones, but i can't see why.