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

[Dave Messina]

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