[Bioperl-l] PAML files

Filipe Garrett fgarret at ub.edu
Mon Dec 18 15:01:38 EST 2006

Hi Jason,

This question is related with the one I made previously today.
I need to run codeml with 3 tree topologies. I looked on codeml module 
but it only accepts one tree as input so I thought of using the codeml 
module to prepare all the files and then I would just have to run the 
codeml with the new tree file in batch. But for that I need to know 
which one is the ctl file.

any idea?

Jason Stajich wrote:
> They are temporary names so they are deliberately random and there is no 
> intention of you needing them after a run since it to be cleaned up on 
> the fly. We use an internal method for generating tempfiles that takes 
> care of cleanup afterwards.  I suppose since we do all the work within a 
> temp directory that is cleaned up, one could have a fixed name for the 
> tree, alignment, and ctl files but honestly we never expect people to be 
> reading these filenames as they are intended to be transient.
> What problem are you having that you need the filename?
> -jason
> On Dec 18, 2006, at 11:18 AM, Filipe Garrett wrote:
>> Hi all,
>> does anyone knows how to get the name of the .ctl file created by the 
>> PAML module? Inside the tmp directory there are 2 files with random 
>> names (tree and ctl). Why do they have random names?? Wouldn't it be 
>> easier to assign them a fixed name?? For instance "codeml.ctl" and 
>> "tree.nwk"??
>> thanks in adv,
>> FG
>> _______________________________________________
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> --
> Jason Stajich
> jason at bioperl.org <mailto:jason at bioperl.org>
> http://jason.open-bio.org/

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