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

Chris Fields cjfields at illinois.edu
Sat Jan 31 00:15:21 EST 2009


I'm pretty sure PAML 4.2 won't parse if the output is similar to 4.0.   
There is an outstanding bug reported here:

http://bugzilla.open-bio.org/show_bug.cgi?id=2482

chris

On Jan 30, 2009, at 7:43 PM, Jason Stajich wrote:

> 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
>
>
>
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