[Bioperl-l] PAML problem

Daisie Huang 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.

Daisie


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. 
>
> Jason 
> 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 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368 
> > 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 
> University 
> > Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814 
> > Email: d... at ibio.jp <javascript:> Tel: +81 80 3268 9713 
> > 
> > _______________________________________________ 
> > Bioperl-l mailing list 
> > Biop... at lists.open-bio.org <javascript:> 
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
> Jason Stajich 
> jason.... at gmail.com <javascript:> 
> ja... at bioperl.org <javascript:> 
>
>
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>


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