[Bioperl-l] PAML problem

Du, Peng du at ibio.jp
Tue Sep 4 07:34:37 EDT 2012


Hi Daisie,

Problem got fixed~~
Thank you ^_^.

On Tue, Sep 4, 2012 at 8:05 PM, Du, Peng <du at ibio.jp> wrote:
> 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



-- 

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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