[Bioperl-l] Bio::DB::CUTG behaving weird

Stefan Kirov skirov at utk.edu
Mon Jun 27 10:20:01 EDT 2005

I am trying to debug it right now and I have some limited success. I 
will let you know what may be wrong as soon as I can. By the way, do you 
minde adding some simple functionality which may be useful to this 
module such as 3-way table consisting of AA name, symbol and letter as in:
If you don't have the time I can add this as well (if you consider it 
useful of course).

Richard Adams wrote:

> Stefan,
> I'm looking into it although I don't have access to either of those  OSs.
> Does the test script (t/DBCUTG.t) run OK on both systems?
> I imagine the error is coming from  the fact that the parser is trying 
> to parse the mitochondrial table
> and I will try to sort out why that isn't parsing properly. Basically 
> all the DBCUTG module does to cope
> with a non-unique species is just select the  first in the list based 
> on regexp matching, this is usually the most likely choice.
> I'll put in some hopefully more challenging tests in the test script 
> to help find the bug. If you can run your script with
> $db->verbose(1) set (using the CVS version) and send me the output I 
> can look into it more...
> Best wishes,
> Richard

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