screed.Record(..., quality=None) should not set 'quality'

[ctb]

Right now, you can't pass 'None' in with 'record' in order to create a Record without a quality entry. Should be able to.

[luizirber]

When you create a new Record like this:

>>> screed.Record(name="test", sequence="ACGT", quality=None)

the result should be:

1. {'name': 'test', 'sequence': 'ACGT', 'quality': None}
2. {'name': 'test', 'sequence': 'ACGT', 'quality': ""}
3. {'name': 'test', 'sequence': 'ACGT'}

1 is the current result, 2 is consistent with khmer.ReadParser.

[ctb]

I think #3 personally. We use hasattr(r, 'quality') throughout the current codebase.

[luizirber]

Then we have a conflict with #1484, I had the impression we should keep an empty quality attribute?

[ctb]

Well, umm, I think (3) personally. Which fits with a lot of existing Python code. shrug It's up for discussion.

[luizirber]

I agree with 3, but we need to discuss how similar we want both screed.Record and khmer.Read to be, and if we should then remove the quality attribute from khmer.Read if it doesn't have quality.

[ctb]

On Thu, Oct 06, 2016 at 05:36:04PM -0700, Luiz Irber wrote:

I agree with 3, but we need to discuss how similar we want both screed.Record and khmer.Read to be, and if we should then remove the quality attribute from khmer.Read if it doesn't have quality.

Yes, see #769. I personally think that the Python code is more likely to
reflect good syntax/use because it's easier to change, so would go with
screed's approach. But then again I've had more of a hand in screed's approach,
so that's probably to be expected....

Are there any drawbacks to the approach?

[betatim]

I think we can make khmer.ReadParser behave like option 3. I'd start with adding https://docs.python.org/3/c-api/typeobj.html#c.PyTypeObject.tp_getattro to the Read type that checks if the stored string is "" or not to decide.

[ctb]

This already works, c.f. #1559.