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.
numpy successfully installed using:
sudo apt-get install python3-numpy