Thanks for suggesting the reference "Coping with Scoping". It was both informative and easy to read. Now that that problem is cleared up I can see that my program is crashing in the last foreach block. This is the error message I will get:

MSG: unable to parse location successfully out of UO3722.1:1..548, 
ignoring feature (seqid=MMKCNAS2)
______________
Can't call method "location" on an undefined value at 
/usr/local/lib/perl5/site/5.6.1/Bio/SeqIO/FTHelper.pm line 136.
[download]

Now what does that mean? And is it the first or second problem that is causing the code to be aborted? Thanks again for your help, speedster.

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