[Biopython] Start positions for local pairwise alignments?

[Peter Cock]

On Mon, Sep 3, 2012 at 10:31 AM, Jan T Kim <jttkim at googlemail.com> wrote:
> Dear All,
>
> after reading a pairwise alignment computed using the EMBOSS water
> program, is it possible to find out the indices of the sequences in
> the local alignment within the input sequences?
>
> ...
>
> I can't seem to find that information anywhere either in the resulting
> Bio.Align.MultipleSeqAlignment object, or in the SeqRecord objects
> that it contains.
>
> So, am I looking at the wrong place?

No, these number are not currently being parsed. This applies to
some of the other file formats in AlignIO too, because we (still)
don't have an agreed way to store this in our object model.

Last time I used this parser, I was probably using needle rather
than water, where these are global alignments so you don't need
the start/end values.

Peter