[Bioperl-l] SeqIO fails on masked sequences

[Wes Barris]

Nathan Haigh wrote:

> 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

Hi Nathan,

I was just curious if you have found anything out regarding this?

> 
> 
> 
>>-----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
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> 
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-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au