[Bioperl-l] Saving Codeml Output file

[Jason Stajich]

File::Copy module cp() works too instead of using a system call which will be more OS independent.

If you don't want the temp files cleaned up you can set the save_tempfiles to true, e.g.
$obj->save_tempfiles(1)
before your call run().
and also have the program report the tempdir like

print $obj->tempdir;

See Bio::Tools::Run::WrapperBase for the other inherited methods for the Run classes.

Dave Messina has debugged some of PAML4 recently, the problem is that there is constant changes in the output format of the mlc and other report flies making it difficult to insure this constantly works. It is a reason we should try and get HyPhy support working as that will allow for probably better standardized running and output.

Jason
On Mar 7, 2012, at 2:55 AM, Janet Young wrote:

> Lorenzo Carretero Paulet <locarpau <at> upvnet.upv.es> writes:
> 
>> 
>> Thanks Jason,
>> Ok, I see. That's what I was triying at the beggining. This runs OK in my
>> scripts  for
>> branch-specific models. However, when I try branch-site models (NSsites > 0)
>> and try to parse the results using
>> my $model_result= $paml_result->get_NSSite_results
>> I start to have problems.
>> 
>> That's why I was trying to save the mlc output file and parse it, instead of
>> parsing directly the Bio::Tools::Phylo::PAML object.
>> 
> 
> 
> Hi Lorenzo,
> 
> I just ran into a similar issue (trying to save the output files 
> for debugging purposes) and found your email thread.  I managed 
> to retrieve the output files by adding this code (after the 
> "$codeml_factory->run" step).
> 
> my $tempdir = $codeml_factory->tempdir;
> system("cp $tempdir/* .");
> 
> Maybe that'll help me debug some issues I'm having with parsing a minority of 
> my paml runs - we'll see. It might be beyond my skills.
> 
> Janet
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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