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

[Jon manning]

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