[Biopython-dev] Alignment problem. bug?

[Peter]

On Tue, Jul 8, 2008 at 9:51 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Jul 7, 2008 at 9:30 PM, Sebastian Bassi <sbassi at gmail.com> wrote:
>> I would like to confirm that this is a bug ot not. If I get
>> confirmation, I would fill it in bugzilla.
>
> It does look like a bug to me...

I've reproduced this using Clustalw 2.0.8 (online at the EBI) and with
 Clustalw 2.0.9 (installed locally).  It was a problem parsing Clustal
files where the first line of the consensus was blank (and would
probably affect both Clustal W 1.83 too).

I think I have fixed this with Bio/AlignIO/ClustalIO.py revision: 1.12

Could you update this file and re-test please Sebastian?  Also, may I
add a test alignment file based on your example to CVS please?

Thanks,

Peter