[Bioperl-l] PAML/Codeml parsing

Stefan Kirov stefan.kirov at bms.com
Tue Dec 4 16:51:51 EST 2007

Jason Stajich wrote:
> should be fixed.
> $ cvs log -r HEAD Bio/Tools/Phylo/PAML.pm
> revision 1.56
> date: 2007/11/01 14:52:56;  author: jason;  state: Exp;  lines: +21 -14
> Parsing PAML4 and PAML3.15 should work now.  Dealing with variable
> order for the sequences and summary results in
> the top of the MLC files
Yes, this is the version I have and in some cases the sequences do not
get parsed. I have missed this commit. I will try to assemble a testcase
and send it. Cannot promise when but will try to do it tomorrow. My gut
feeling so far is that the parser works whenever there are gaps in the
alignment, otherwise it does not. PAML surely has very peculiar format.
Thanks again!
> On Dec 4, 2007, at 11:25 AM, Stefan Kirov wrote:
>> Jason Stajich wrote:
>>> PAML4 breaks our PAML parser right now because the order of things in
>>> the result file has changed.  Now sequences precede the information
>>> about the version or the program run.  This means that $result-
>>>> get_seqs() fails because we don't parse the sequences.
>>> We'll see what we can do, but as usual with supporting 3rd party
>>> programs it is brittle when file formats change.  Th
>>> -jason
>>> -- 
>>> Jason Stajich
>>> jason at bioperl.org
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> Jason,
>> I saw a commit after this post on codeml, but not on PAML.pm- I assume
>> this is not fixed, am I correct?
>> Thanks!
>> Stefan

More information about the Bioperl-l mailing list