Hi,
I am new bioinformatics using Python and have encountered a problem importing Biopython to Anaconda. Please help.
As far as I can tell, I have installed the package using Conda and it is visible on my root environment. However, I still can't seem to import it when using Jupyter notebooks in Anaconda.
1 answer
My preferred way to install python packages (conda or otherwise).
Install conda, and ensure that you start the right interpreter (the binary installed by conda). Result of which python should return a path including your conda path. For example, for me it's:
joehealey@Joes-MacBook-Pro~ $ which python
/Users/joehealey/Applications/miniconda2/bin/python # NOT /usr/local/bin or some other path
joehealey@Joes-MacBook-Pro~ $ python
Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:05:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
Then:
$ python -m pip install biopython
Should work and will ensure that all the paths etc. are set up correctly. It's basically the same process outlined in my previous answer: A: Run a Python program in Ubuntu
This is assuming of course that the error I think you're having is the right one. As Wouter pointed out, we need more info.
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Please elaborate on which commands you used for installing the packages, which commands you use for importing and which errors you get. We can't read minds, unfortunately.