Help with Biopython and Anaconda

Question

[Ed]

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.

[WouterDeCoster]

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.

Answer 1

[Joe]

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.

[Ed]

Thanks for your help, and sorry for the lack of detail (I'm very new to this).

I believe that's sorted it now..

[Joe]

If that's solved your issue, be sure to accept the answer so that the thread doesn't remain open ended.

[WouterDeCoster]

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

• How To Ask Good Questions On Technical And Scientific Forums
• How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
• How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.