Question

I installed Biopython, but I am unable to get the computer to recognize the modules. For example, I create a text file in Komodo like this:

from Bio.Alphabet import IUPAC
from Bio import Seq
my_prot=Seq.Seq("AGTACACTGGT",IUPAC.protein)

and run it in terminal and receive:

Traceback (most recent call last):
  File "bio.py", line 1, in <module>
    from Bio.Alphabet import IUPAC
ImportError: No module named Bio.Alphabet

For the record, I can’t get modules to import in interactive mode either. The documentation states that I can append the module search path by exporting to an environmental variable called PYTHONPATH (like with PATH), but when I type ‘env’ into the terminal, I see no environmental variable of the sort. I’m a biologist–not a computer scientist or programmer. Please bear with my naiveté if this sounds like nonsense.

Answer 1

You must find in which directory situated the module that you needs (Bio) and then add the path to the directory to PYTHONPATH.

$ export PYTHONPATH=/usr/local/bio-python/

Instead of /usr/local/bio-python/ you must specify the path that you’ve found.

To find the module you must use something like:

$ find / -name \*Bio\*

That is just an example. Of course it would be better if you could give some additional information (e.g. where you’ve installed the module and so on).