[Bioperl-l] PAML/Codeml parsing
jason at bioperl.org
Tue Dec 4 16:36:09 EST 2007
should be fixed.
$ cvs log -r HEAD Bio/Tools/Phylo/PAML.pm
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 Stajich
>> jason at bioperl.org
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> I saw a commit after this post on codeml, but not on PAML.pm- I assume
> this is not fixed, am I correct?
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