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How to use the script #2

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arcys opened this issue Apr 14, 2015 · 1 comment

arcys commented Apr 14, 2015

Hi,
I am new in python and interested in using this python code to convert the .biom file from hdf5 format to a json one. However it does not sucess:

python HDF5toJSON.py my_file.biom my_fileJ.biom

Traceback (most recent call last):
File "HDF5toJSON.py", line 26, in
h5file = open_file(sys.argv[1])
NameError: name 'open_file' is not defined

Can you show an example on how to use the python code? Thanks a lot!!

ChenMinQi commented May 2, 2015

You should "pip install tables".

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