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

Chris Fields cjfields at uiuc.edu
Wed Jan 10 12:17:40 EST 2007


> Cook, Malcolm wrote:
> > 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 ;)
> 
> Sounds good to me. I didn't understand before why you'd have 
> different start and end offsets, but now all is clear :)

Same here.  Commit away I say!

chris



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