[Bioperl-l] PROPOSED new method Bio::Range->offsetStranded

Cook, Malcolm MEC at stowers-institute.org
Wed Jan 10 12:07:21 EST 2007


Hi Chris,
 
In part of a pipeline to design oligo microarray for detecting alternate
splice sites, I build 0-length features which identify the location of
all 5' and 3' splice sites (as inferred from flybase GFF gene,
transcript, mRNA, exon features) and then offset these feature to create
a region flanking it, which is then taken as the target of an oligo
design process.

I'm sure I could re-conceptualize my approach, but, as implemented, it
works a treat.

My thinking is influenced by my Excel's object model (VBA), which has
Offset as a destructive method of Excel.Range (of excel cells).

I suppose any algorithm that used a 'sliding window' could possibly
benefit from Bio::Range->offsetStranded.

Cheers,

Malcolm Cook (poised to commit ;)
  

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu] 
> Sent: Wednesday, January 10, 2007 10:10 AM
> To: Cook, Malcolm; 'bioperl list'; muilu at ebi.ac.uk; bix at sendu.me.uk
> Subject: RE: [Bioperl-l] PROPOSED new method 
> Bio::Range->offsetStranded
> 
> Malcolm,
> 
> I don't have a problem with it.  Just curious, but what would 
> it be used
> for?
> 
> chris
> 
> > Hi,
> > 
> > I'd like to commit changes to Bio::RangeI which defined 
> > offsetStranded to allows the following tests to pass in Bio/Range.t
> > 
> > $r = Bio::Range->new(-start => 30, -end => 40, -strand => 
> > -1); ok ($r->offsetStranded(-5,10)->toString, '(20, 45) 
> > strand=-1'); ok ($r->offsetStranded(+5,-10)->toString, '(30, 
> > 40) strand=-1'); $r->strand(1); ok 
> > ($r->offsetStranded(-5,10)->toString, '(25, 50) strand=1'); 
> > ok ($r->offsetStranded(+5,-10)->toString, '(30, 40) strand=1');
> > 
> > 
> > Here's the implementation.
> > 
> > =head2 offsetStranded
> > 
> >     Title    : offsetStranded
> >     Usage    : $rnge->ofsetStranded($fiveprime_offset,
> > $threeprime_offset)
> >     Function : destructively modifies RangeI implementing object to
> >                offset its start and stop coordinates by 
> > values $fiveprime_offset and
> >                $threeprime_offset (positive values being in 
> > the strand direction).
> >     Args     : two integer offsets: $fiveprime_offset and
> > $threeprime_offset
> >     Returns  : $self, offset accordingly.
> > 
> > =cut
> > 
> > sub offsetStranded {
> >   my ($self, $offset_fiveprime, $offset_threeprime) = @_;
> >   my ($offset_start, $offset_end) = $self->strand() eq -1 ? 
> > (- $offset_threeprime, - $offset_fiveprime) : 
> > ($offset_fiveprime, $offset_threeprime);
> >   $self->start($self->start + $offset_start);
> >   $self->end($self->end + $offset_end);
> >   return $self;
> > };
> > 
> > 
> > I'll commit tomorrow unless I'm told 'that would be a mistake'.
> > 
> > Cheers,
> > 
> > --Malcolm
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 



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