[Bioperl-l] Bio::Variation::RNAChange

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Jul 6 09:20:26 EDT 2007


Hi Nat,

These modules have not been touched for a while and were developed for a 
specific task. A revire is defiitely in order.

The way RNAChange->label was written, it should return 'inframe' when given no 
alleles, but 'no change' would actually be better.

The multiple alleles were originally though to be a good idea, but the 
vocabulary for labels was developed for single allele, only, The use of the 
module ended up being limited to single allele, so add_allele() behaviour was  
conveniently ignored but not removed. :(

	-Heikki



On Friday 06 July 2007 14:54:33 Nathan S. Haigh wrote:
> Nathan S. Haigh wrote:
> > I'm taking a look at the tests for Bio::Variation::RNAChange.
> >
> > If you create a new oject without arguments:
> > my $obj = Bio::Variation::RNAChange->new();
> >
> > What do you expect the following to return:
> > $obj->label();
> >
> > I thought it would probably be:
> > 'inframe'
> >
> > However you get:
> > 'inframe, deletion'
> >
> > Can anyone in the know explain what behaviour would be expected?
> >
> > Cheers
> > Nath
>
> Following on from this, AAChange has the following two methods:
> add_Allele() and allele_mut()
>
> It appears that allele_mut is only capable of remembering 1 allele at a
> time, whereas add_Allele() is provided to add support for mutliple
> alleles - is that correct?
>
> However, add_Allele() also calls allele_mut(), such that mutliple calls
> to add_Allele will result in the overwriting of the allele being
> remembered by allele_mut(). Things are further complicated by the fact
> that label() uses allele_mut() to decide on the label to return.
> Shouldn't label know aout multiple alleles set by multiple calls to
> add_Allele?
>
> It may be my lack of understanding alleles and what these classes are
> intending to do, but trying to rewrite the test scripts to improve code
> coverage has let me a little confused!
>
> Thanks
> Nath
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
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