[Biopython] Seq object ungap method

[Peter]

On Fri, Nov 20, 2009 at 2:29 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> Something we discussed last year was adding an ungap method
> to the Seq object. e.g.
> http://lists.open-bio.org/pipermail/biopython/2008-September/004523.html
> http://lists.open-bio.org/pipermail/biopython/2008-September/004527.html
>
> As mentioned earlier this month on the dev mailing list,
> http://lists.open-bio.org/pipermail/biopython-dev/2009-November/006983.html
> I actually made the time to implement this, and posted it on a
> github branch - you can see the updated Bio/Seq.py file here:
> http://github.com/peterjc/biopython/blob/ungap/Bio/Seq.py
>
> I've included a copy of the proposed docstring for the new Seq object
> ungap method at the end of this email, which tries to illustrate how this
> would be used.

In the absence of any further comments (thanks Eric for your reply on
the dev list), I've made an executive decision to check this into the trunk.
This will make it much easier for people to test the new ungap method.

I remain open to feedback (e.g. naming of the method) and we can even
remove this before the next release if that turns out to be the consensus.

Peter