anaconda 中的 biopython，而不是 jupyter notebook

Question

I am trying to install biopython in Jupyter Notebook, Anaconda, Ubuntu 16.04. I follow the procedure in biopython website and it runs on python.

Python 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> 

However, it does not work on Jupyter Notebook.

from Bio.PDB.PDBParser import PDBParser

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-ada1f75604ba> in <module>()
      1 # biopython testing
----> 2 from Bio.PDB.PDBParser import PDBParser

ModuleNotFoundError: No module named 'Bio'

conda list also how biopython installed.

biopython                 1.72             py36h04863e7_0    anaconda
blas                      1.0                         mkl    anaconda
ca-certificates           2019.1.23                     0  
certifi                   2019.3.9                 py36_0  
intel-openmp              2019.3                      199    anaconda
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgfortran-ng            7.3.0                hdf63c60_0    anaconda
libstdcxx-ng              8.2.0                hdf63c60_1  
mkl                       2019.3                      199    anaconda
mkl_fft                   1.0.10           py36ha843d7b_0    anaconda
mkl_random                1.0.2            py36hd81dba3_0    anaconda
ncurses                   6.1                  he6710b0_1  
numpy                     1.16.2           py36h7e9f1db_0    anaconda
numpy-base                1.16.2           py36hde5b4d6_0    anaconda
openssl                   1.1.1b               h7b6447c_1  
pip                       19.0.3                   py36_0  
python                    3.6.8                h0371630_0  
readline                  7.0                  h7b6447c_5  
setuptools                40.8.0                   py36_0  
sqlite                    3.27.2               h7b6447c_0  
tk                        8.6.8                hbc83047_0  
wheel                     0.33.1                   py36_0  
xz                        5.2.4                h14c3975_4  
zlib                      1.2.11               h7b6447c_3  

Is there any reason why it is not working? I appreciate any help.

Answer 1

Turns out the solution is to install Jupyter Notebook in the anaconda environment first.

conda install -c anaconda jupyter
conda install -c anaconda biopython

Now biopython could be called within the environment.

Answer 2

open anaconda navigator,click on environments,choose not installed,search the biopython package in the search box. select biopython to install.

Answer 3

maybe you created a conda env using conda create -n xxx but have not added it to the jupyter kernel? (that means you install Biopython not in base conda env but you choose the base jupyter kernel ?

try this cmd

conda activate your_biopython_env
conda install ipykernel
python -m ipykernel install --user --name your_biopython_env --display-name "your_biopython_env"

then refresh jupyter-notebook using F5 and change the kernel to your_biopython_env

can it work for u?