[Bioperl-l] SeqFeatureI.pm: get all starts and ends from 'join'

[Jan Aerts]

Thanks, that solved my problem. (I read the HOWTO 'till only a few lines
before that solution...)

jan.

On Mon, 2004-06-07 at 14:56, Marc Logghe wrote:
> Hi Jan,
> 
> > -----Original Message-----
> > From: Jan Aerts [mailto:jan.aerts at wur.nl]
> > Sent: maandag 7 juni 2004 14:44
> > To: bioperl-l at portal.open-bio.org
> > Subject: [Bioperl-l] SeqFeatureI.pm: get all starts and ends 
> > from 'join'
> > 
> > 
> > Hi all,
> > 
> > I'm trying to extract all exon boundaries from a genbank file. The
> > relevant feature of the file looks like this:
> > mRNA   complement(join(1..238,718..763,1552..1677,1925..2004))
> > 
> > Using $feat->start and $feat->end, I can get the numbers 1 
> > and 2004, but
> > I can't seem to get hold of the other exon/intron boundaries? 
> > Can anyone
> > tell me how to get to these numbers?
> #You can get to the location object with
> my $loc = $feat->location;
> #In this specific case it will be a split location object
> foreach my $sloc ($loc->sub_Location)
> {
>   print join( ',', $loc->start, $loc->end), "\n";
> }
> 
> But it is all better explained in the howto you can find at:
> http://bioperl.org/HOWTOs/html/Feature-Annotation.html#location
> 
> HTH,
> Marc
>