Python for Bioinformatics: Another head-scratcher

Friday, October 29, 2010

Another head-scratcher

I know about keywords in Python. You can't do this:

>>> and = 3
  File "<stdin>", line 1
    and = 3
      ^
SyntaxError: invalid syntax

But I do like simple names for objects and functions. I acquired this habit from Stroustrup's book on the C++ language, 10 years ago, before I even knew about Python.

However, I must remember not to make the names too familiar. For example, yesterday I rashly named a script new.py. And this single line caused problems that had me scratching my head:

import matplotlib.pyplot as plt

Apparently matplotlib also uses the name new for a module (although I haven't actually located it):

Traceback (most recent call last):
  File "new.py", line 1, in 
    import matplotlib.pyplot as plt
  File "/Library/Python/2.6/site-packages/matplotlib/pyplot.py", line 6, in 
    from matplotlib.figure import Figure, figaspect
  File "/Library/Python/2.6/site-packages/matplotlib/figure.py", line 18, in 
    from axes import Axes, SubplotBase, subplot_class_factory
  File "/Library/Python/2.6/site-packages/matplotlib/axes.py", line 2, in 
    import math, sys, warnings, datetime, new
  File "/Users/telliott_admin/Desktop/new.py", line 1, in 
    import matplotlib.pyplot as plt
AttributeError: 'module' object has no attribute 'pyplot'

[UPDATE:

new.py is not a matplotlib module, it's in the standard library, but it's deprecated. It provides a way to instantiate a new object without calling __init__. I'm not sure what situation you would want to use it for other than what it says in the docs.

There is one use of new in axes.py but I don't understand it:

_subplot_classes = {}
def subplot_class_factory(axes_class=None):
    # This makes a new class that inherits from SubclassBase and the
    # given axes_class (which is assumed to be a subclass of Axes).
    # This is perhaps a little bit roundabout to make a new class on
    # the fly like this, but it means that a new Subplot class does
    # not have to be created for every type of Axes.
    if axes_class is None:
        axes_class = Axes

    new_class = _subplot_classes.get(axes_class)
    if new_class is None:
        new_class = new.classobj("%sSubplot" % (axes_class.__name__),
                                 (SubplotBase, axes_class),
                                 {'_axes_class': axes_class})
        _subplot_classes[axes_class] = new_class

    return new_class