[Bioperl-l] PAML problem

Du, Peng du at ibio.jp
Tue Sep 4 07:05:59 EDT 2012


Hi Daisie,

Thank you for your reply.
Where could I get the bioperl-live you mentioned? Is it something
equivalent to bioperl core package?
If it is, do I need to reinstall the whole bioperl package?

Thank you.
Peng

On Fri, Aug 17, 2012 at 3:38 AM, Daisie Huang <daisieh at gmail.com> wrote:
> 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 Tel: +81 80 3268 9713
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Biop... at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Jason Stajich
>> jason.... at gmail.com
>> ja... at bioperl.org
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Biop... at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 

Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713


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