Maybe as a NuleotideSequenceRead class (derived from NucelotideSequence),
but not as part of the existing objects.


On Sun, Mar 9, 2014 at 2:15 PM, Daniel McDonald <notifications@github.com>wrote:

> In bipy/core/iterator.py:
>
> > +
> > +        gen = instance_of_sequence_iterator()
> > +
> > +        item1 = gen.next()
> > +        seq1 = item1['Sequence']
> > +
> > +        item2 = gen.next()
> > +        seq2 = item2['Sequence']
> > +
> > +        id(item1) == id(item2) # True
> > +        item1 == item2         # True
> > +
> > +        id(seq1) == id(seq2)   # False
> > +        seq1 == seq2           # False
> > +    """
> > +    def __init__(self, seq, qual=None, transform=None, valid_id=True,
>
> bah, I'm torn. I like keeping the SequenceIterator independent of the
> BiologicalSequence as including it makes this code more complex as the
> BiologicalSequence has no notion of quality scores. The issue is that,
> casting to BiologicalSequence then decouples sequence from qual, which
> makes it more awkward to express transforms like reverse complement.
> Leaving this cast up to the developer, or the success_f callback for
> Workflow is an easy option which keeps this code more lean and mean.
>
> @jrrideout <https://github.com/jrrideout> @gregcaporaso<https://github.com/gregcaporaso>,
> do you think it would be useful to include quality in the
> BiologicalSequence object?
>
> --
> Reply to this email directly or view it on GitHub<https://github.com/biocore/bipy/pull/106/files#r10415749>
> .
>