[Bioperl-l] Bio::Factory::SequenceFactoryI SYNOPSIS example

Hilmar Lapp hlapp at gmx.net
Fri Apr 11 19:19:44 EDT 2008


Thanks, applied. -hilmar

On Apr 11, 2008, at 3:39 PM, Adam Sjøgren wrote:
> On Fri, 11 Apr 2008 11:35:54 -0400, Hilmar wrote:
>
>> On Apr 11, 2008, at 4:53 AM, Adam Sjøgren wrote:
>
>>>> my $seqbuilder = Bio::Seq::SeqFactory->new('type' =>
>>>> 'Bio::PrimarySeq');
>
>> You need to prefix the argument with a dash: '-type', not 'type'.
>> Otherwise, it assumes that the class you want instantiated is
>> 'type.pm'.
>
> I guess that means I should submit a patch for the SYNOPSIS. Attached.
>
>
>    Thanks,
>
>     Adam
>
>
> Index: Bio/Factory/SequenceFactoryI.pm
> ===================================================================
> --- Bio/Factory/SequenceFactoryI.pm	(revision 14654)
> +++ Bio/Factory/SequenceFactoryI.pm	(working copy)
> @@ -20,7 +20,7 @@
>  # get a Bio::Factory::SequenceFactoryI object like
>
>      use Bio::Seq::SeqFactory;
> -    my $seqbuilder = Bio::Seq::SeqFactory->new('type' =>  
> 'Bio::PrimarySeq');
> +    my $seqbuilder = Bio::Seq::SeqFactory->new('-type' =>  
> 'Bio::PrimarySeq');
>
>      my $seq = $seqbuilder->create(-seq => 'ACTGAT',
>  				  -display_id => 'exampleseq');
>
> -- 
>  "Well, I'm a moon around you"                                Adam  
> Sjøgren
>                                                           
> asjo at koldfront.dk
>
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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