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.

In reply to Re: Re: Help with code by speedo
in thread Help with code by speedo

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