[Bioperl-l] Bio/SeqFeature/Annotated proposed patch

Chris Fields cjfields at uiuc.edu
Fri Jan 19 15:57:34 EST 2007


I don't have a problem with it, though I wonder if the '.' has  
something to do with GFF formatting.  Does this pass tests?

Chris

On Jan 19, 2007, at 2:30 PM, Cook, Malcolm wrote:

> I ran across this problem:
>
> Setting the score of a feature to 0 (zero) cuases it to really be  
> set to
> '.'.
>
> I'm poised to apply the following patch.
>
> Any objections?
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>
> Index: Annotated.pm
> ===================================================================
> RCS file:
> /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Annotated.pm,v
> retrieving revision 1.36
> diff -c -r1.36 Annotated.pm
> *** Annotated.pm	16 Oct 2006 16:20:38 -0000	1.36
> --- Annotated.pm	19 Jan 2007 20:25:01 -0000
> ***************
> *** 425,432 ****
>         $self->add_Annotation('score', $term);
>     }
>
> !   $self->score('.') unless ($self->get_Annotations('score')); # make
> sure we always have something
> !
>     return $self->get_Annotations('score');
>   }
>
> --- 425,439 ----
>         $self->add_Annotation('score', $term);
>     }
>
> !   #$self->score('.') unless ($self->get_Annotations('score')); #  
> make
> sure we always have something
> !
> !   # malcolm.cook at stowers-institute.org is not sure why we want to
> !   # 'make sure we always have something', but, in any case, the  
> above
> !   # sets the score to '.' when there is an explicit score of 0,  
> which
> !   # can't be correct, so, re-writing to use 'has_tag' as follows:
> !
> !   $self->score('.') unless $self->has_tag('score'); # make sure we
> always have something
> !
>     return $self->get_Annotations('score');
>   }
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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