[Bioperl-l] Bio::Align::DNAStatistics

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Mon May 19 23:18:38 EDT 2008


The version you have is quite old, Sendu added _set_from_args() just 
after the one you have. Current one has the following id:

$Id: RootI.pm 11557 2007-07-05 15:46:22Z sendu $

You should checkout a more recent version of bioperl.

Mauricio.

Steve Beckstrom-Sternberg wrote:
> Hi Mauricio,
> 
> I checked out RootI.pm in Bio::Root and did not find the _set_from_args()
> method.  Below is the version of RootI.pm.  Is it too old?
> 
> # $Id: RootI.pm,v 1.69.4.4 2006/10/02 23:10:23 sendu Exp $
> 
> 
> 
> Thanks,
> 
> Steve
> 
> 
> 
> On 5/19/08 7:07 PM, "Mauricio Herrera Cuadra"
> <arareko at campus.iztacala.unam.mx> wrote:
> 
>> Hi Steve,
>>
>> The _set_from_args() method is implemented in the Bio::Root::RootI
>> class, which is a module from the bioperl (core) distribution, not from
>> bioperl-run. In order to use any of the bioperl-run wrappers you'll need
>> to install the core bioperl distribution as well.
>>
>> Hope this helps.
>>
>> Regards,
>> Mauricio.
>>
>> sbeckstrom at tgen.org wrote:
>>> Hi Jason,
>>>
>>> The problem seems to be specific to Clustalw.pm, with version listed here:
>>> (# $Id: Clustalw.pm,v 1.53 2007/06/14 15:23:08 sendu Exp $)
>>>
>>> Below is subroutine "new", which calls _set_from_args in line 409 of
>>> Clustalw.pm:
>>>
>>> sub new {
>>>     my ($class, at args) = @_;
>>>     my $self = $class->SUPER::new(@args);
>>>
>>>     $self->_set_from_args(\@args, -methods => [@CLUSTALW_PARAMS,
>>>                                                @CLUSTALW_SWITCHES,
>>>                                                @OTHER_SWITCHES],
>>>                                   -create => 1);
>>>     
>>>     return $self;
>>> }
>>>
>>> The error states that it cannot find the _set_from_args method.
>>> And I cannot find a subroutine called _set_from_args in Clustalw.pm.
>>> What am I missing?
>>>
>>> Thanks,
>>>
>>> Steve
>>>
>>>
>>>
>>>
>>> On 5/16/08 4:15 PM, "Jason Stajich" <jason at bioperl.org> wrote:
>>>
>>>> Sounds like an old bioperl version mixture, but I'm not sure, you'll
>>>> need to let us know what version of bioperl you have installed.
>>>>
>>>> Please include the mailing list in these types of questions so others
>>>> can help.
>>>>
>>>> -jason
>>>> On May 15, 2008, at 1:49 PM, Steve Beckstrom-Sternberg wrote:
>>>>
>>>>> Hi Jason,
>>>>>
>>>>> I have bioperl-run installed and I am testing pairwise_kaks.PLS.
>>>>> I am getting an error from Clustalw.pm, and it looks like this is
>>>>> because
>>>>> subroutine ³new² is calling a subroutine that is not there
>>>>> (_set_from_args).
>>>>>
>>>>> Here is the error:
>>>>>
>>>>> ./pairwise_kaks.PLS
>>>>> Can't locate object method "_set_from_args" via package
>>>>> "Bio::Tools::Run::Alignment::Clustalw" at
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm
>>>>> line 409.
>>>>>
>>>>> Here is the version of Clustalw.pm:
>>>>> # $Id: Clustalw.pm,v 1.53 2007/06/14 15:23:08 sendu Exp $
>>>>>
>>>>>
>>>>> Any direction on how to resolve this?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Steve
>>>>>
>>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
> 
> 
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM


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