[BioPython] Clustalw.parse_file errors

[Peter]

On Tue, Aug 5, 2008 at 10:39 PM, Nick Matzke <matzke at berkeley.edu> wrote:
> Thanks for the help Peter, it really is a great tutorial!
>
> I've replaced just the ClustalIO.py file as you suggested, and it parses
> both the example.aln and protein.aln files.

Good :)

> However I tried an ClustalW-formatted alignment file I made awhile ago with
> my own data and still got the star_info error:
>
> AttributeError: Alignment instance has no attribute '_star_info'
>
> But my file could be weird.  Does the _star_info error indicate alphabet
> issues or something?

The _star_info is a nasty private variable used to store the ClustalW
consensus, used if writing the file back out again in clustal format.
The error suggests something else has gone wrong with the consensus
parsing... (and shouldn't be anything to do with the alphabet).

Could you file a bug, and (after filing the bug) could you upload one
of these example files to the bug as an attachment please?

Peter