[Bioperl-l] to_FTstring() for Bio::Graphics::FeatureBase

Lincoln Stein lstein at cshl.edu
Fri Jan 26 18:12:49 EST 2007


Hi Jason,

Ack, embarassing. I'll fix this somehow and commit when I think the changes
are right. Feel free to make suggestions.

Lincoln

On 1/26/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Let me rephrase - I can see where this might not be the correct fix. I
> have Bio::DB::SeqFeature objects which are CDS objects, I want to print out
> their location with to_FTstring, but it is only returning min..max for the
> location.
>  I guess for something that is a Segment there is only one value
> (min..max) that should be presented.
>
> imagine I've done:
>  for my $gene ( $segment->features('gene') ) {
>   for my $mRNA ( $gene->get_SeqFeatures('mRNA') {
>    for my $CDS ( $mRNA->get_SeqFeatures('CDS') {
>      print $CDS->location->to_FTstring();
>    }
>   }
>  }
>
>
> Also - I note that if I call $CDS->length on a reverse-strand feature I
> get a negative length.
>
> So Feature::Base would need to be changed to this:
>
> sub length {
>   my $self = shift;
>   return $self->high - $self->low + 1;
> }
>
> instead of
>
> sub length {
>   my $self = shift;
>   return $self->end - $self->start + 1;
> }
>
>
> -jasonOn Jan 26, 2007, at 2:52 PM, Jason Stajich wrote:
>
> Lincoln:
>
> Right now the code for Bio::Graphics::FeatureBase implementation of the
> LocationI interface method, to_FTstring is:
>
> sub to_FTstring {
>   my $self = shift;
>   my $low  = $self->min_start;
>   my $high = $self->max_end;
>   return "$low..$high";
> }
>
> So strand is thrown away.  Is it legitimate to modify this to return
> $high..$low when strand < 0?
>
> -jason
>
>
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
>
>
>
>


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Lincoln D. Stein
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