[Biopython] Codeml parser in Biopython?

[Peter]

On Tue, Sep 14, 2010 at 3:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Sep 14, 2010, at 4:04 AM, Peter wrote:
>> On Tue, Sep 14, 2010 at 9:02 AM, natassa <natassa_g_2000 at yahoo.com> wrote:
>>>
>>> Here is an example output, but this caan differ depending on the model used
>>> (there are several models for Branch, Site, BranchSite, but all are pretty
>>> standard)
>>
>> Thanks - that looks possible to parse, but not very easy (especially if the
>> codeml output changes slightly between versions).
>
> Just a warning from those experienced with paml parsers (bioperl): the
> output is notoriously shifty even between minor releases (sections get
> reordered, etc), so pretty much any parse needs to accommodate that.
> It's extremely frustrating.

Thanks Chris - I was afraid of that. It sounds like parsing plain text
NCBI BLAST output, but worse.

Do you know if anyone has asked about codeml outputting something
nicer to parse instead? e.g. Nexus or any kind of XML?

Peter