[Bioperl-l] question about the PAML module in bioperl

[Jason Stajich]

I think it is probably that PAML 4.2 is not supported - we have not  
been able to keep up with the constant change in output format in  
PAML's more recent versions.  If you go back to PAML 3 it should work.  
You should also give bioperl 1.6 a try, although I'm not confident  
that it will work right now.

A proper testing of many of PAML's use-case outputs and validation of  
the parsing across multiple-versions of PAML is on the list of things  
that need to be done, but I doubt it is something I'll have much time  
for right now.

-jason

On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote:

>
> Dear Dr. Stajich,
>
> I work in a bioinformatic group at the University of Torino, Italy,  
> and I write to you this email regarding a problem with the PAML  
> module in bioperl.
>
> My goal is to evaluate the Ka/Ks ratio for a group of sequences and,  
> to this end, I found a very nice example perl code based on bioperl:
>
> http://www.bioperl.org/wiki/HOWTO:PAML
>
> I tried to implement the example, but, unfortunately, it doesn't  
> work (see the attached script).
>
> In particular, it seems that the part of the code relative to the  
> clustalw alignment procedure works properly, but the second part,  
> relative to the PAML execution, always stops with the following  
> message:
>
> ........
> .........
> ..........
> Sequence:110     Score:1115
> Sequence:42     Score:1468
> Sequence:52     Score:1752
> Sequence:96     Score:1495
> Alignment Score -1235112
> GCG-Alignment file created      [/tmp/BtFAMhn879/L0AkU4W1UJ]
>
> -------------------- WARNING ---------------------
> MSG: There was an error - see error_string for the program output
> ---------------------------------------------------
> Can't call method "get_MLmatrix" on an undefined value at  
> prova_KaKs_bioperl.pl line 78, <GEN2> line 1099.
>
> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system.
>
> Do yo have any suggestion to solve this issue ?
>
> Could you suggest me a way to obtain a working code that is able to  
> perform such analysis ? Do you have a piece of running code to  
> obtain the KaKs ratio for a group of sequences ?
>
> Thanks in advance for your help,
>
> Davide
>
>
>
>
> ---------------------------------
> Davide Cora', PhD
> Department of Theoretical Physics
> University of Torino
> Via P. Giuria 1
> 10125, Torino, Italy
>
> email: cora at to.infn.it
> web: http://www.to.infn.it/~cora/
> phone: +39 011 6707238
> --------------------------------- 
> <yeast_cDNA_Known_Known.txt><prova_KaKs_bioperl.pl>

Jason Stajich
jason at bioperl.org