[Bioperl-l] SeqIO fails on masked sequences
nathanhaigh at ukonline.co.uk
Thu Dec 16 06:21:57 EST 2004
Ok, the "bug" seems to have been introduced in the last update to Bio::PrimarySeq.pm (v1.83) where X was added to the list of
ambiguous characters in the _guess_alphabet subroutine.
Brian - do you remember why/what this was for?
> -----Original Message-----
> From: Marc Logghe [mailto:Marc.Logghe at devgen.com]
> Sent: 16 December 2004 10:44
> To: nathanhaigh at ukonline.co.uk; Wes Barris
> Cc: Bioperl Mailing List
> Subject: RE: [Bioperl-l] SeqIO fails on masked sequences
> > When I use the script you supplied, I get the exception shown below.
> > I'll try to get to the bottom of this.
> > In the meantime, what OS are you both using and what version
> > of Bioperl?
> Ah, yes that explains. Too much fiddling with PERL5LIB is not good ;-)
> I did not realize I was acutally using bioperl 1.4.0. There it worked.
> It fails indeed when using bioperl-release-1-5-0-rc1.
> Apologies for confusing you people.
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