parsing a multiple sequence alignment file

Question

[imaditi1987]

Hi,

I have generated clustal alignment files which show a single small aligned region of about 2-25 bases. Can we parse the clustal file using biopython in a way that in output it only shows those 25 aligned bases.

[Coryza]

Not sure what you mean... give a example please of how it is now, and how you would like to see it.

[imaditi1987]

(1)

This is how it looks currently (1) and I want the output (2)

(2)

[Coryza]

It's blank

[venu]

better show some alignment data and also how you want the output. Seems possible with simple script, if I understand properly.

Answer 1

[glihm]

Hello there,

Sure you can --> Biopython CookBook, section 6.4.1. ;)

And yes, it's blank.