[Biopython-dev] [Biopython - Bug #3320] (New) Bio.Phylo.PAML KeyError in codeml

[Brandon Invergo]

I'll take care of this now...

-brandon

On Thu, 2012-02-02 at 03:22 +0000, redmine at redmine.open-bio.org wrote:
> Issue #3320 has been reported by Timothee Flutre.
> 
> ----------------------------------------
> Bug #3320: Bio.Phylo.PAML KeyError in codeml
> https://redmine.open-bio.org/issues/3320
> 
> Author: Timothee Flutre
> Status: New
> Priority: Normal
> Assignee: 
> Category: 
> Target version: 
> URL: 
> 
> 
> I get the following error while using codeml in Bio.Phylo.PAML (same error for options "fix_rho" and "rho"):
> 
> <pre>
> Traceback (most recent call last):
>   File "./PamlAnalysis.py", line 42, in main
>     cml.read_ctl_file(genericCtlFile)
>   File "/home/src/BIOPYTHON/lib/python/Bio/Phylo/PAML/codeml.py", line 133, in read_ctl_file
>     raise KeyError, "Invalid option: %s" % option
> KeyError: 'Invalid option: fix_rho'
> </pre>
> 
> I resolved the problem by adding the following two lines in the file Bio/Phylo/PAML/codeml.py at the lines 63-64:
> 
> <pre>
>                         "fix_rho": None,
>                         "rho": None,
> </pre>
> 
> Such errors do not happen when using the example file "codeml.ctl" available with the "PAML":http://abacus.gene.ucl.ac.uk/software/paml.html archive (v4.4 or v4.5) as this file does contain neither the option "fix_rho" nor "rho". But these options are present in PAML "documentation":http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf (see p.33-34). Moreover, these two options are present in the file Bio/Phylo/PAML/baseml.py at the lines 49-50.
> 
> Do I need to fork the biopython repository on github and make the changes myself?
> 
> 
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