[Bioperl-l] different syntaxes for SeqI constructor and Factory constructor?

Chris Fields cjfields at uiuc.edu
Thu Dec 7 14:44:19 EST 2006


On Dec 7, 2006, at 1:32 PM, Brian Osborne wrote:

> Chris,
>
> The latest StandAloneBlast takes "dashed parameters", as in:
>
>  @params = (-database => 'swissprot',-outfile => 'blast1.out');
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>
> Or
>
>  my $factory = Bio::Tools::Run::StandAloneBlast->new(-program  
> =>"wublastp",
>                                                      - 
> database=>"swissprot",
>                                                      -e => 1e-20);
>
> So that's why I asked "what version?"
>
> Someone made the change to allow dashes in @params a few months ago  
> and I
> believe that that someone was you!
>
> Brian O.

Nope, I plead innocent (at least to this!).  I haven't made any  
commits to StandAloneBlast.  These were added in by Torsten (see  
commits 1.59, 1.60), so you'll need to blame/thank him...

http://tinyurl.com/y7ym9g

So they're now a bit more consistent.  That's not to say  
StandAloneBlast doesn't need some major revisions....

BTW, I didn't see a post from you asking about the version.

Chris


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