[Biopython-dev] [Biopython] Subclassing Seq and SeqRecord

[Jose Blanca]

What I mean is this:
http://github.com/JoseBlanca/biopython/commit/d4c87365f614de2d69d800dc63d0cc25087d96dc

I would like to change the Seq() and SeqRecord() for self.__class__
There are places already in Seq in which self.__class__ is used. But this is 
not the case in all instances. I think that this would be a reasonable 
change.

> >
> >    def _set_qual(self, qual):
> >        '''It stores the quality in the
> > letter_annotations['phred_quality']'''
> > self.letter_annotations["phred_quality"] = qual
> >    def _get_qual(self):
> >        '''It gets the quality from letter_annotations['phred_quality']'''
> >        return self.letter_annotations["phred_quality"]
> >    qual = property(_get_qual, _set_qual)
>
> I can see how adding a property makes accessing the PHRED
> qualities much easier.

Yes, that's just a convenience method. I used to have my own class with this 
property and now I'm trying to use SeqRecord instead but adding this method 
to ease the change.

> >    def __add__(self, seq2):
> >        '''It returns a new object with both seq and qual joined '''
> >        #per letter annotations
> >        new_seq = self.__class__(name = self.name + '+' + seq2.name,
> >                                 id = self.id + '+' + seq2.id,
> >                                 seq  = self.seq + seq2.seq)
> >        #the letter annotations, including quality
> >        for name, annot in self.letter_annotations.items():
> >            if name in seq2.letter_annotations:
> >                new_seq.letter_annotations[name] = annot + \
> >                                         seq2.letter_annotations[name]
> >        return new_seq
>
> This bit is much less clear to me - you completely ignore any
> features. Was it written before I added the __add__ method
> to the original SeqRecord (expected to be in Biopython 1.53)?
Yes, it was added much earliear. I'll remove it as soon as the Biopython 
SeqRecord has one.

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)