[Bioperl-l] SeqFeatureI.pm: get all starts and ends from 'join'
jan.aerts at wur.nl
Mon Jun 7 09:10:06 EDT 2004
Thanks, that solved my problem. (I read the HOWTO 'till only a few lines
before that solution...)
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:
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