[Bioperl-l] PAML problem
daisieh at gmail.com
Thu Aug 16 14:38:25 EDT 2012
I'm not sure which PAML component caused this particular outcome, but the
bugs and fixes I pushed to bioperl-live might fix this. When will those get
pulled into the master?
If those particular fixes don't help, I'd be happy to take a peek at the
originator's code and see if it's a quick re-parsing fix.
On Tuesday, June 26, 2012 6:37:55 PM UTC-7, Jason Stajich wrote:
> Peng -
> This module needs a person who's sole job is to keep tracking bugs and
> updating it with new versions of the program. so far it has burned out
> several developers on working on it since it not stable.
> I am not sure what the answer is to the problem, but often it depends on
> the extra parameters used as this changes the order of the output making it
> hard to parse.
> So I don't have a solution for you except that you'll have to post the bug
> and the problem output mlc file to redmine and hope that we can entice some
> developers to bang their head against this some more.
> On Jun 26, 2012, at 6:28 PM, Du, Peng wrote:
> > Hi everyone,
> > I am using bioperl to parse paml output, and I saw this
> > ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> > MSG: Unknown format of PAML output did not see seqtype
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw
> > STACK: Bio::Tools::Phylo::PAML::_parse_summary
> > /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:461
> > STACK: Bio::Tools::Phylo::PAML::next_result
> > /usr/local/share/perl/5.10.1/Bio/Tools/Phylo/PAML.pm:270
> > STACK: main::cal_dn_ds dn_ds.pl:131
> > STACK: dn_ds.pl:44
> > ----------------------------------------------------------------
> > I googled and found that, it was caused by PAML version
> > incompatibility. I tried 3.13, 3.14, 4.1, 4.2, 4.5 and none of them
> > worked. Could someone tell me which version is fine?
> > My bioperl version is 1.006001. Thank you very much.
> > --
> > Peng Du
> > Graduate School of Information Science and Technology, Hokkaido
> > Kita 14 Nishi 9 Kita-ku, Sapporo, Japan 060-0814
> > _______________________________________________
> > Bioperl-l mailing list
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> Jason Stajich
> Bioperl-l mailing list
More information about the Bioperl-l