[Bioperl-l] Bio::Tools::SeqStat

[Heikki Lehvaslaiho]

Peter,

I noticed that SeqStat module choked on some Bio::RichSeq entries coming
from EMBL/Genbank. The reason is that SeqStat imposes strict alphabets
which for RNA sequences is (A,U,G,C) but the incoming sequence contains
Ts.

I fixed that in the HEAD so that  _is_alphabet_strict(),
get_mol_wt() and count_monomers() internally convert s/T/U/g.
However, I am not 100% sure that this is what users expect. Your call.

I ran into this while cleaning scripts. Try:

bala ~/src/bioperl-live/scripts/seqstats> perl gccalc.PLS -f embl
../../t/data/ar.embl


	-Heikki


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     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
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