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pythonbioinformaticsanacondasamtools

pysam module import results in error

struggling to define what is causing this error.

Have anaconda installed and used conda install pysam, worked for a bit but suddenly getting this error 

>>> import pysam
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Nick/anaconda/lib/python2.7/site-packages/pysam/__init__.py", line 125, in <module>
    [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
AttributeError: 'module' object has no attribute '__all__'

Took a look inside the file and the corresponding code is 

# hack to export all the symbols from csamtools
__all__ = \
    csamtools.__all__ + \
    ctabix.__all__ + \
    cvcf.__all__ +\
    [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
    ["Pileup" ]

Any idea on what is causing this???

Solution

  • Ok, Uninstalled using conda, also uninstalled using pip, then pip reinstalled seemed to fix it.

    Still getting some errors with other parts of the module but working on a fix.

    Thanks for advice!