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

Jason Stajich jason.stajich at duke.edu
Mon Mar 7 13:48:49 EST 2005

I think you are talking about _guess_alphabet?

You can always override the _guess_alphabet method - I posted a soln to 
this last month.

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 Stajich
jason.stajich at duke.edu

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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