[BioPython] problems parsing alignment files

[Brad Chapman]

Hey all;

[Ashleigh reports errors in parsing Clustalw and PIR files]

Me:
> If you could send me the NBRF and ALN files (off-list), I can
> have a look and see if I can figure where they are failing and try
> to get everything fixed.

To follow up to the list -- I got the files and just now squished
the bugs. Here were the problems:

=> The clustalw format didn't accept question marks in title names.

=> The NBRF/PIR parser didn't handle Clustalw format PIR, which is
valid but different then the PIR files you can download.

Fixes for both of these are in CVS and I also squashed some other
bugs in the PIR parsing that I found.

Thanks again to Asleigh for the report.
Brad