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

[redmine at redmine.open-bio.org]

Issue #3320 has been reported by Timothee Flutre.

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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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