How do I set the PYTHONPATH on Cygwin?

Question

In the Biopython installation instructions, it says that if Biopython doesn't work I'm supposed to do this:

export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopython'

I tried doing that in Cygwin from the ~ directory using the name of the Biopython directory (or everything of it past the ~ directory), but when I tested it by going into the Python interpreter and typing in

From Bio.Seq import Seq

It said the module doesn't exist.

How do I make it so that I don't have to be in the Biopython directory to be able to import Seq?

Answer 1

You wrote "(or everything of it past the ~ directory)". I think you need to use the full directory path. And ~ isn't expanded immediately after a ':', so use $HOME instead:

export PYTHONPATH = $PYTHONPATH":$HOME/directory/where/you/put/Biopython"

(Note the use of double rather than single quotes so $HOME is expanded.)

Answer 2

You can add the directory to your sys.path list

import sys
biopythondir = '/where/you/put/biopython'
if biopythondir not in sys.path:
  sys.path.append(biopythondir)

# import seq

Or, for a more elegant solution than mucking around with environment variables and sys.path, see how to use .pth files to extend sys.path.