fixed one of the script usage tests
Merge branch 'biom_pep8' of https://github.com/teravest/qiime into emilys_biom
one one of the usgage tests is still failing
usage tests pass now!!!!
Merge branch 'biom_pep8' of https://github.com/teravest/qiime into emilys_biom
Removing taxa summary funcs and test, we will rely on biom's functions
addressing comments
Merge pull request #52 from teravest/emilys_biom

fixed one of the script usage tests
API Use HDF5 in parallel/test_map_reads_to_reference.py
API/BUG Use load_table
STY: PEP8 import statements
Merge pull request #55 from antgonza/format

Format
Merge pull request #57 from ElDeveloper/map-parallel-reads-hdf5

Map parallel reads hdf5
Merge branch 'beta-metrics-hdf5' of github.com:ElDeveloper/qiime into beta-metrics-hdf5
API/BUG: Use lists instead of ndarrays

If using ndarrays you could compromise compatibility in some versions of
numpy where comparing arrays of strings is not supported and you would
get a traceback for doing something like this:

>>> import numpy as np
>>> a = np.array(['yo', 'samples', "it's"], dtype='str')
>>> b = np.array(['yo', "it's", 'samples'], dtype='str')
>>> np.array_equal(a, b)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/yova1074/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages/numpy/core/numeric.py", line 2119, in array_equal
    return bool(equal(a1,a2).all())
AttributeError: 'NotImplementedType' object has no attribute 'all'

Note that this is happening in 1.7.1 (I was only able to reproduce this
problem in a RHEL installation.