[Biopython] Mapping positions in a pairwise alignment

[Lenna Peterson]

Hi Lior,

I don't know if you've resolved this yet - it's been several months! But I
am not aware of any way to do this in Biopython.

I was doing a similar task so I made a gist using your example:

https://gist.github.com/lennax/9925c08804a57bb5ef72

Cheers,

Lenna

On Tue, Jun 16, 2015 at 3:35 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:

> Hi all,
>
> I have a pairwise alignment of protein sequences, created with Bio.pairwise2,
> something like this:
>
> C-GGLK-GAPFLAC||||||||||||||
> CHG--KTGASFLQC
>
> I would like to know which position in the subject sequence is aligned to
> which position in the query sequence. In this example if the top sequence
> is the subject than I would like to know that position 1 in subject is
> aligned to position 1 in query, 2 is aligned to 3, 5 to 4, 6 to 6 etc...
>
> Does Biopython have this functionality, or do I have to write my own
> function? Any suggestions?
>
> Thanks!
>
>
>
>
>
>
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