[Bioperl-l] PAML files

Jason Stajich jason at bioperl.org
Mon Dec 18 14:33:32 EST 2006

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?

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

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