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

Richard Adams Richard.Adams at ed.ac.uk
Mon Jun 27 09:56:46 EDT 2005

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,


Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK

Tel: 44 131 651 1084
richard.adams at ed.ac.uk

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