Re: Re: Help with code

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.
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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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Re: Re: Re: Help with code by myocom (Deacon) on Jul 18, 2001 at 22:14 UTC
In general, messages like "`Can't call method "location" on an undefined value ...`" mean that you are trying to call a method on an object that doesn't exist (either you haven't created it with its constructor or the object has been destroyed). In this case, it appears that the code that is trying to call a method is in one of the Bio::SeqIO modules. That doesn't rule your code out entirely, but it does make it harder to track down the problem. You might check the docs for that series of modules to see if there are any hints there.	[reply] [d/l]

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Re: Re: Re: Help with code
by myocom (Deacon) on Jul 18, 2001 at 22:14 UTC

In general, messages like "Can't call method "location" on an undefined value ..." mean that you are trying to call a method on an object that doesn't exist (either you haven't created it with its constructor or the object has been destroyed). In this case, it appears that the code that is trying to call a method is in one of the Bio::SeqIO modules. That doesn't rule your code out entirely, but it does make it harder to track down the problem. You might check the docs for that series of modules to see if there are any hints there.

[reply]
[d/l]