[Biopython] subclassing SeqRecord

[Björn Johansson]

Hi, and thanks for the answer,

I could use the annotations but it is a dict and I suppose that I
could not be entirely sure that whatever key I choose is not already
used? This is also an exercise in python an inheritance to teach me
this technique.

What added to my confusion in my old code was that I initiated a
SeqRecord object with a SeqRecord object as the seq property. The seq
property can apparently be anything for which there is a len()
method..?

I ended up doing a class that can be initialized with a string, Seq
object or a SeqRecord object.

from Bio.Alphabet.IUPAC import ambiguous_dna
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq

#Subclassing of the SeqRecord class

class Primer(SeqRecord):
    def __init__(self, seq=None, annealing_position=None, *args, **kwargs):

        self.annealing_position = annealing_position

        if isinstance(seq,Seq):
            seq.alphabet = ambiguous_dna
            SeqRecord.__init__(self, seq, *args, **kwargs)

        elif isinstance(seq,str):
            SeqRecord.__init__(self,Seq(seq,ambiguous_dna), *args,
**kwargs)

        elif isinstance(seq,SeqRecord):
            SeqRecord.__init__(self,
                               seq.seq,
                               seq.id,
                               seq.name,
                               seq.description,
                               seq.dbxrefs,
                               seq.features,
                               seq.annotations,
                               seq.letter_annotations)
        else:
            raise TypeError("the seq property needs to be a string, a
Seq object or a SeqRecord object")



a = Primer("aaa",11,"id1","name1")

b = Primer(Seq("ccc"),22,"id2","name2")

c = Primer(SeqRecord(Seq("ttt")),33)


print a.annealing_position
print b.annealing_position
print c.annealing_position

print a.reverse_complement().seq
print b.reverse_complement().seq
print c.reverse_complement().seq












On Tue, Apr 26, 2011 at 17:15, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> 2011/4/26 Björn Johansson <bjorn_johansson at bio.uminho.pt>:
> > Hi, I tried to subclass the SeqRecord object to make it take a new parameter
> > which is a int describing the annealing position for a primer. I tried the
> > code below, but it does not produce the result I want and it is also ugly,
> > mostly where indicated. This question may be more about Python the
> > BioPython, but I run into the wall here.
>
> What I would expect you to do is just store this integer in the existing
> SeqRecord's annotations dictionary.
>
> > The comments in the code point out where it goes wrong.
> >
> > I have RTFM but in the Python docs, but I still did not figure this one out.
> > I suspect that I am complicating things.
> >
> > If someone knows how to do this, I would be grateful!
>

>
> You probably should use isinstance(x, SeqRecord) rather than type(x).
>
> Peter



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