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

[Dave Messina]

Great, glad to hear that. Thanks for letting us know about the problem!

Dave




On May 5, 2010, at 8:58, Dimitar Kenanov wrote:

> 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
>