All right, here's some wacky ideas from my recent alignments tutorial
work. These are all minor issues that I stumbled over.
After discussion I'll provide patches or enter these into the issue
tracker (or not, based on the discussion).
---
First, NLMSA objects don't support iteration:
Traceback (most recent call last):
File "foo.py", line 29, in <module>
for x in al:
File "cnestedlist.pyx", line 1676, in pygr.cnestedlist.NLMSA.__getitem__
KeyError: 'key must be a sequence interval or python slice object'
...and they don't report a reasonable error, either. (The above error
is caused by an attempt to use __getitem__ with an integer, part of
Python's automatic sequence protocol.)
I think we should either define an __iter__ function that says "don't do
this!" *or* we should support the full range of dict functions on NLMSA.
I vote for the former for 0.8, and the latter for post-0.8.
Thoughts?
--
Second, NLMSASlice objects don't behave like a full mapping object,
either. I think that's OK for now but we should fix this, post-0.8.
--
Third, NLMSASlice objects could use a more informative __repr__. How
about including the sequence ID (slice.seq.id) in there?
--
And, finally, NLMSASlice keys(), values(), and edges() all take a large
(and identical) set of parameters. It might be nice to set these
parameters *once* for a given NLMSA instance, and then have those
default settings apply for future queries:
al = cnestedlist.NLMSA(...)
al.set_default_query_params(mingaps=4)
slice = al[seq].keys() # => mingaps=4 automatically used in keys()
I can see this getting confusing, though, as I wouldn't expect them to
be persistent across NLMSA instances. I'm curious about what people
think.
Hmm, perhaps one way to do this would be to provide an NLMSA wrapper
object:
al = cnestedlist.NLMSA(...)
wrap = NLMSAParamWrapper(al, mingaps=4)
slice = wrap[seq].keys() # => mingaps=4 automatically used in keys()
Since I want to provide an NLMSA wrapping anyway (so that we can e.g.
wrap several NLMSAs into one container) this might fit well in there.
--
cheers,
--titus
--
C. Titus Brown, c...@msu.edu
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