[Bioperl-l] gap/ambiguous character only sequences: Bio::PrimarySeq

[Jason Stajich]

I think you are talking about _guess_alphabet?

You can always override the _guess_alphabet method - I posted a soln to 
this last month.
http://portal.open-bio.org/pipermail/bioperl-l/2005-February/018253.html

Does that work for you?  It warns instead of throws when it is all 
gapped.  You can make it even quieter if you like of course.

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Mar 3, 2005, at 10:26 AM, Jon manning wrote:

> Hi All,
>
> For a lot of the stuff I'm doing at the moment I'm chopping up
> alignments and playing with the bits etc. I've had to nobble
> Bio::PrimarySeq to allow the resulting gap-only sequences in
> Bio::LocatableSeq- I understand the rationale behind this check, and
> it's a useful default, but could we perhaps have an option to allow
> tolerance instead? If such exists, I'd be grateful if someone could
> point me in the right direction!
>
> Thanks,
>
> Jon
>
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