[Biopython] Codeml parser in Biopython?

[Chris Fields]

On Sep 14, 2010, at 4:04 AM, Peter wrote:

> Hi Anastasia,
> 
> On Tue, Sep 14, 2010 at 9:02 AM, natassa <natassa_g_2000 at yahoo.com> wrote:
>> Hi Peter,
>> 
>>> 
>>> Could you post a short example of the kind of output you are looking at?
>>> 
>> 
>> 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).
> 
>>> 
>>> Can you get codeml to output what you need in another format, such as NEXUS?
>>> 
>> 
>> Haven't tried that, but as you can see, this is a very verbose output and
>> NEXUS does not seem an option.
> 
> At first glance, the NEXUS format could hold a lot of that information.
> Another possibility might be phyloXML. However, you are at the mercy
> of the codeml tool and what it supports. I might be worth politely asking
> the author(s) about supporting one of these more standard formats as
> a optional output.
> 
>> Ultimately, I want to parse this to get all the information I need in a
>> tabulated file. I am still working out what exactly I need (there are standard
>> values to get out, as LnL, branch length, Dn/Ds, but it also depends on the type
>> of downstram analysis). I will now work on the pypaml class and modify the
>> original code to make it more generic (it seems that it only works for Site
>> Models).
> 
> Note that Ziheng Yang's pypaml code is licensed under the GPL v3, so
> unless he agrees to re-license it we cannot include it in Biopython.
> 
>> Will let you know, was just wondering if there was already a solution.There is
>> one in Bioperl, but heard it is very slow and in any case, I don't understand
>> much of perl....
> 
> I don't know much Perl either ;)
> 
> Peter

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.

chris