[Bioperl-l] Bio::DB::CUTG behaving weird
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:
> 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,
More information about the Bioperl-l