[Bioperl-l] get_MLmatrix

Jason Stajich jason.stajich at gmail.com
Wed Mar 21 16:58:14 EDT 2012

This is undoubtably due to changes in the output format between versions.

Aaron and I aren't maintaining this but I am CC-ing the mailing list to see if someone else is working on it.

The roads to solution are 
 - fix the parser
 - run an earlier version of PAML that can be parsed with the current code

Sorry there isn't a better solution but there is no adhered to standard for output by PAML so it requires a developer to constantly track the program and its output and reverse engineer it to keep the parser working. 

For the second error, I am not sure if you are calling the function on right object -- maybe there is a mistake in the documentation relative to the API now, I'm not sure.
The object Bio::Tools::Phylo::PAML::ModelResult has a kappa method so can you check what object type you have when you are calling kappa
if you are calling 
then add debugging print to your code
warn( ref($result), "\n");


On Mar 21, 2012, at 1:41 PM, Vaclav Janousek wrote:

> Hi,
> I'd like to use the bioperl packages to parse the codeml mlc file (runmode
> = -2). However, the parser retrieves empty field for _mlmatrix
> (get_MLmatrix). I am using the newest version of PAML 4.5 so there might be
> some change in the output file which causes the parser cannot recognise the
> part containing the parameter estimates as well as the lnL value. Is there
> any chance to fix this problem?
> Also, the method get_model_params doesn't work - compiler complaints the
> method cannot be located via package Bio::Tools::Phylo::PAML::Result. So
> there is no way (in case the get_MLmatrix would work) how to obtain kappa
> estimate (at least according the documentation for the
> Bio::Tools::Phylo:PAML::Codeml).
> Thanks a lot,
> Vaclav
> -- 
> Vaclav Janousek
> E-mail: vaclav.janousek at natur.cuni.cz
> Department of Zoology
> Charles University in Prague
> Faculty of Science
> Albertov 6, 128 43 Praha 2
> www.natur.cuni.cz/en

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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