[Bioperl-l] question about Bio::Tools::Run::Genewise

[Dimitar Kenanov]

Hi Dave,
thank you for the tip. Now it works like a charm :)

Greetings
Dimitar


On 05/02/2010 05:59 PM, Dave Messina wrote:
> Hi Dimitar,
>
> The syntax you want is:
>
> # Build a Genewise alignment factory
> my $factory = Bio::Tools::Run::Genewise->new();
>
> # turn on the quiet switch
> $factory->QUIET(1);
>
> # @genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
> my @genes = $factory->run($protein_seq, $genomic_seq);
>
>
> This turns out be incorrectly documented on the man page, at least in part:
>    
>> Available Params:
>>
>> NB: These should be passed without the '-' or they will be ignored,
>> except switches such as 'hmmer' (which have no corresponding value)
>> which should be set on the factory object using the AUTOLOADed methods
>> of the same name.
>>
>>    Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
>>    Alg      [-kbyte,-alg]
>>    HMM      [-hmmer]
>>    Output   [-gff,-gener,-alb,-pal,-block,-divide]
>>    Standard [-help,-version,-silent,-quiet,-errorlog]
>>      
>
> That is, these don't work as expected:
>
> 	$factory->quiet;
> 	$factory->quiet(1);
>
> due to a conflict with the quiet() method inherited from Bio::Tools::Run::WrapperBase.
>
> And passing a true value such as 1 is in fact necessary or the switch-type parameters won't be set.
>
>
> So it looks like the parameter passing system in B::T::R::Genewise might benefit from some revision. I'll put this on the bugtracker.
>
>
> Dave
>
>    


-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
email: dimitark at bii.a-star.edu.sg
tel: +65 6478 8514