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

Nathan S. Haigh n.haigh at sheffield.ac.uk
Fri Jul 6 08:54:33 EDT 2007


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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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