[Bioperl-l] SeqIO fails on masked sequences

[Nathan Haigh]

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?

Nathan


> -----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.
> Cheers,
> Marc
> ---
> avast! Antivirus: Inbound message clean.
> Virus Database (VPS): 0451-1, 14/12/2004
> Tested on: 16/12/2004 10:47:57
> avast! is copyright (c) 2000-2003 ALWIL Software.
> http://www.avast.com
> 
> 

---
avast! Antivirus: Outbound message clean.
Virus Database (VPS): 0451-1, 14/12/2004
Tested on: 16/12/2004 11:21:54
avast! is copyright (c) 2000-2003 ALWIL Software.
http://www.avast.com