[BioPython] Installation of Biopython 1.40b on Windows XP system (newbee on (bio)python and programming)

[E.M.Wielhouwer]

Dear All,

As beginner in programming I picked up O'Reilly's "Learning Python" because 
there was a package called BioPython with nice tools for free of use of 
which I'm interested in as Biomedical Researcher. Bought both books 
(learning and programming python, however, following each of examples per 
chapter of "learning python" I stumbled upon a problem that I can't 
overcome which make me desperate due to the lack of knowledge on this 
subject. (below also questions on the installation of biopython on my 
windows XP machine)

As read at page 270 I tried to follow your example on importing scripts 
outside the python installation directory but I failed. I hope you might 
want to help me out here I'm really stuck aon this subject. Below I 
describe what I've done but first some settings of python.

----
Python version: PythonWin 2.4.1 (#65, Mar 30 2005, 09:33:37) [MSC v.1310 32 
bit (Intel)] on win32. Portions Copyright 1994-2004 Mark
                       Hammond (mhammond at skippinet.com.au) - see 
'Help/About PythonWin' for further copyright information.

Operating system: Windows-XP SP1

Program locates at:             C:\\Prgrmmr\\Python24
Specific MyScript 
path  C:\Prgrmmr\Python24\MyPythonpaths.pth           (this includes two 
lines of code: # .pth file for My own Scripts
                                                                                                                         and: 
C:\Prgrmmr\MyCode\ )
Location of my scripts: C:\\Prgrmmr\\MyCode
----

Here is my output from Python (pythonwin - IDE mode).

----
 >>> import sys
 >>> sys.path
['', 'C:\\WINDOWS\\System32\\python24.zip', 'C:\\Documents and 
Settings\\Gandalf', 'C:\\Prgrmmr\\Python24\\DLLs', 
'C:\\Prgrmmr\\Python24\\lib', 'C:\\Prgrmmr\\Python24\\lib\\plat-win', 
'C:\\Prgrmmr\\Python24\\lib\\lib-tk', 
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\pythonwin', 
'C:\\Prgrmmr\\Python24', 'C:\\Prgrmmr\\MyCode', 
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\reportlab', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\Numeric', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\PIL', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32', 
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32\\lib']
---- continued below----

['', 'C:\\WINDOWS\\System32\\python24.zip',
'C:\\Documents and Settings\\Gandalf',
'C:\\Prgrmmr\\Python24\\DLLs',
'C:\\Prgrmmr\\Python24\\lib',
'C:\\Prgrmmr\\Python24\\lib\\plat-win',
'C:\\Prgrmmr\\Python24\\lib\\lib-tk',
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\pythonwin',
'C:\\Prgrmmr\\Python24',
'C:\\Prgrmmr\\MyCode',
'C:\\Prgrmmr\\Python24\\Lib\\site-packages\\reportlab',
'C:\\Prgrmmr\\Python24\\lib\\site-packages',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\Numeric',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\PIL',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32',
'C:\\Prgrmmr\\Python24\\lib\\site-packages\\win32\\lib']

----continued-----
 >>> import Prgrmmr.MyCode.mod
Traceback (most recent call last):
   File "<interactive input>", line 1, in ?
ImportError: No module named Prgrmmr.MyCode.mod
 >>>
----

Similar result is obtained even when the __init__.py file is included in 
the C:\\Prgrmmr and C:\\Prgrmmr\\MyCode directory.

The __init__.py file includes the following text:       #File: 
Python\__init__.py
                                                         print 'Python init'
                                                         x=1

I hope you can help me out on this (most likely I forgot something 
mentioned in the book (which I assume)),


A few other things which seems to be difficult for me on Brad's biopython 
installation manual.

First, it's not clear to me if I should have additional libraries aside the 
ones described in Brad's Manual?

Second, (manual 3.3.2 Reportlab install) How about rl_accel 0.52, PyRXP 
1.05, etc. , etc. has that also to be installed?
www.biopython.org/docs/install/Installation.html#htoc18

Third (manual 3.4) should I install MySQL from www.mySQL.com prior to the 
install of MySQLdb or not at all? 
www.biopython.org/docs/install/Installation.html#htoc20

Third, (manual 3.4) because I've got a windows XP OS I need to compiler the 
psycog library (or do I call this differently) for that, where do I get a 
(VC++ 6) compiler from (might be a stupid question)?
www.biopython.org/docs/biosql/python_biosql_basic.html#htoc6

Finally, (manual 4.4)  where goes the documentation, tests, example code 
that exists in the biopython source file biopython-1.40b.zip. Does it have 
to be compiled and how do I do that if 4.5 does not apply? I question this 
due to the reading of section 5, paragraph 3, line 2 "Tests directory 
inside the distribution). 
www.biopython.org/docs/install/Installation.html#htoc31

I'm stuck on this and every bit help is welcome and well appreciated,


Eric