Question

I know that PyPy has problems with Numpy and other stuff in Biopython, but not all BioPython modules use this things…
Somebody knows how import and use the module Bio into PyPy?

Answer 1

You should be able to install it like in a regular Python version. PyPy is already included in Biopython’s integration testing.

An example using virtualenvwrapper:

$ mkvirtualenv -p /usr/bin/pypy biopy
$ workon biopy
$ cd biopython  # or wherever your biopython directory is
$ python setup.py install
$ python -c 'import Bio'

If you don’t see any error messages from the commands above, then it should be working.