I'm trying to install the biopython module on my Ubuntu 12.04 LTS machine (64x). I first upgraded to Python3.3 by installing from source (biopython does not support other versions), that seems ok.
However, I installed some modules using the sudo apt-get install python-module
command but I can't call them from a python shell:
dovah@AsusX501A:~$ python3.3
Python 3.3.5 (default, Mar 12 2014, 02:09:17)
[GCC 4.6.3] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from biopython import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'biopython'
>>> from Bio import * ##as suggested in http://biopython.org/DIST/docs/api/module-tree.html
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'Bio'
As you can see, the modules are installed:
dovah@AsusX501A:~$ sudo apt-get install python-biopython
Reading package lists... Done
Building dependency tree
Reading state information... Done
python-biopython is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
And so is biopython (quite strange though: line 14 says biopython-1.64-py2.7-linux-x86_64.egg
so best hit was found for version 2.7, not 3.3):
dovah@AsusX501A:~$ sudo easy_install -f http://biopython.org/DIST/ biopython
Searching for biopython
Reading http://biopython.org/DIST/
Best match: biopython 1.64
Downloading http://biopython.org/DIST/biopython-1.64.zip
Processing biopython-1.64.zip
Writing /tmp/easy_install-v5LJZz/biopython-1.64/setup.cfg
Running biopython-1.64/setup.py -q bdist_egg --dist-dir /tmp/easy_install-v5LJZz/biopython-1.64/egg-dist-tmp-TruGJH
warning: no previously-included files matching '.cvsignore' found under directory '*'
warning: no previously-included files matching '*.pyc' found under directory '*'
zip_safe flag not set; analyzing archive contents...
Bio.Entrez.Parser: module references __path__
Adding biopython 1.64 to easy-install.pth file
Installed /usr/local/lib/python2.7/dist-packages/biopython-1.64-py2.7-linux-x86_64.egg
Processing dependencies for biopython
Finished processing dependencies for biopython
Are modules specific for a given Python version? Is the system still stuck on Python 2.7? Obviousely I can't simply remove 2.7 unless I want to mess up my whole OS.
Thank you in advance for your help.
EDIT
numpy successfully installed using: sudo apt-get install python3-numpy