[Bioperl-l] PAML/Codeml parsing

Jason Stajich jason at bioperl.org
Tue Dec 4 16:36:09 EST 2007

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

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