On May 8, 2009, at 12:44 PM, Jenny Qing Qian wrote:
>
> I like the option of overwriting the builtin dir() for Python 2.6 or
> later. Is there a way to implement this without descriptors? A way
> that is universally supported by any Python version. What's wrong
> with __getattr__?
Hi Jenny,
I implemented a basic version of this. First, I added __dir__ to
worldbase (the new name for pygr.Data) objects. Thus in Python 2.6
you can do the following:
Python 2.6.1 (r261:67515, Apr 8 2009, 05:56:20)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from pygr import worldbase
>>> dir(worldbase.Bio) # pygr is doing a worldbase query to retrieve
this...
['MSA', 'Seq']
>>> dir(worldbase.Bio.MSA)
['UCSC']
>>> dir(worldbase.Bio.MSA.UCSC)
['bosTau2ToBostau3', 'bosTau3ToBostau4', 'bosTau4_multiz5way',
'calJac1_multiz9way', 'canFam2_multiz4way', 'ce2ToCe4',
'danRer2ToDanrer3', 'danRer3ToDanrer2', 'danRer3ToDanrer4',
'danRer3_multiz5way', 'danRer4ToDanrer3', 'danRer4ToDanrer5',
'danRer4_multiz7way', 'danRer5ToDanrer4', 'dm2ToDm3',
'dm2_multiz15way', 'dm2_multiz9way', 'dm3_multiz15way',
'felCat3_multiz4way', 'fr2_multiz5way', 'galGal2ToGalgal3',
'galGal2_multiz7way', 'galGal3_multiz7way', 'gasAcu1_multiz8way',
'hg17ToHg18', 'hg17_multiz17way', 'hg18ToHg17', 'hg18_multiz17way',
'hg18_multiz28way', 'mm5ToMm6', 'mm5ToMm7', 'mm5ToMm8', 'mm7ToMm5',
'mm7ToMm6', 'mm7ToMm8', 'mm7_multiz17way', 'mm8ToMm7', 'mm8ToMm9',
'mm8_multiz17way', 'mm9ToMm8', 'mm9_multiz30way',
'monDom4_multiz7way', 'ornAna1_multiz6way', 'oryLat1_multiz5way',
'panTro1ToPantro2', 'panTro2ToPantro1', 'ponAbe2_multiz8way',
'rn3ToRn4', 'rn4ToRn3', 'rn4_multiz9way', 'xenTro1ToXentro2',
'xenTro1_multiz5way']
Second, I added a pygr.dir() function that will work with __dir__
methods on any version of Python (on Python 2.6+ it just defaults to
the builtin dir()). So in any version of Python you can do the
following:
Python 2.5.2 (r252:60911, Apr 1 2008, 20:54:02)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from pygr import worldbase, dir
>>> dir(worldbase.Bio) # using pygr.dir()
['Seq', 'MSA']
...etc...
Third, I also added __dir__ support to sqlgraph.TupleO and SQLRow,
which represent SQLTable row objects. e.g.
Python 2.6.1 (r261:67515, Apr 8 2009, 05:56:20)
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from pygr import sqlgraph
>>> t = sqlgraph.SQLTable('music.itunes_in3') # itunes database
loaded in MySQL...
/sw/lib/python2.6/site-packages/MySQLdb/__init__.py:34:
DeprecationWarning: the sets module is deprecated
from sets import ImmutableSet
>>> o = t[1] # get track 1
>>> dir(o) # will reflect the column names in the database table...
['Album', 'Artist', 'BitRate', 'Comments', 'Composer', 'DateAdded',
'DateModified', 'DiscCount', 'DiscNumber', 'Equalizer', 'Genre',
'Grouping', 'Kind', 'LastPlayed', 'LastSkipped', 'Location',
'MyRating', 'Name', 'PlayCount', 'SampleRate', 'Size', 'SkipCount',
'Time', 'TrackCount', 'TrackNumber', 'VolumeAdjustment', 'Year', 'id']
Try it out if you're interested. Get the latest code from my github
repository.
-- Chris
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