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

[Jose Blanca]

> It is a reasonable change, but ONLY if all the subclasses support
> the same __init__ method, which isn't true. For example, the
> Bio.Seq.UnknownSeq subclasses Seq and uses a different __init__
> method signature. This means any change would at a minimum
> have to include lots of fixes to the UnknownSeq

In this case what I do is to create a new __init__ for the inherited class, 
like:

class SeqWithQuality(SeqRecord):
    '''A wrapper around Biopython's SeqRecord that adds a couple of 
convenience methods'''
    def __init__(self, seq, id = "<unknown id>", name = "<unknown name>",
                 description = "<unknown description>", dbxrefs = None,
                 features = None, annotations = None,
                 letter_annotations = None, qual = None):
        SeqRecord.__init__(self, seq, id=id, name=name,
                           description=description, dbxrefs=dbxrefs,
                           features=features, annotations=annotations,
                           letter_annotations=letter_annotations)
        if qual is not None:
            self.qual = qual

    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)

    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


-- 
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)