[BioPython] installation help

[Sevinsky Joel]

Hello,

I am having some strange errors with biopython.  I have downloaded
biopython, reportlab, `egenix-mx-base, and numpy as instructed, and
installed them using python 'setup.py install'.  Aside from some warnings
I did not get any errors.  I was told that I needed to install Martel, but
it appears that Martel is packaged with biopython already.  I saved my
terminal window so you can see the problem.  Here it is:

[sevinsky@atreides sevinsky]$ python
Python 2.2.1 (#1, Sep  9 2002, 09:26:21)
[GCC 3.2 (Mandrake Linux 9.0 3.2-1mdk)] on linux-i386
Type "help", "copyright", "credits" or "license" for more information.
>>> import mxBASE
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: No module named mxBASE
>>> import Bio
>>>


So as user sevinsky I am not able to import mxBASE, but Bio imports fine.
at the end of this message I have my .bashrc so you can see thta the
PYTHONPATH is correct.  Now I switch to root and have different problems.


[sevinsky@atreides sevinsky]$ su root
Password:
[root@atreides sevinsky]# python
Python 2.2.1 (#1, Sep  9 2002, 09:26:21)
[GCC 3.2 (Mandrake Linux 9.0 3.2-1mdk)] on linux-i386
Type "help", "copyright", "credits" or "license" for more information.
>>> import mxBASE
>>> import Bio
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/biopython-1.10/Bio/__init__.py", line 65, in ?
    _load_registries()
  File "/usr/local/biopython-1.10/Bio/__init__.py", line 57, in
_load_registries
    module = __import__("Bio.config.%s" % module, {}, {},
["Bio","config"])
  File "/usr/local/biopython-1.10/Bio/config/DBRegistry.py", line 33, in ?
    from Martel import Parser
  File "/usr/local/reportlab/__init__.py", line 6, in ?
    __doc__="""The Reportlab PDF generation library."""
  File "Martel/Expression.py", line 33, in ?
  File "Martel/Parser.py", line 33, in ?
ImportError: No module named TextTools
>>> from mx import TextTools
>>>


As root, mxBASE imports fine, but Bio does not.  And the line 33 in
Parser.py runs fine on the interpreter as shown.  Strange.  Below are my
.bashrc files for root and sevinsky.  All packages were storted in
/usr/local.


[root@atreides sevinsky]# more /root/.bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi
export
PYTHONPATH=$PATH:/usr/local/reportlab:/usr/local/egenix-mx-base-2.0.4:/us
r/local/Numeric-22.0:/usr/local/biopython-1.10
PATH=/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin
ENV=$HOME/.bashrc
USERNAME="root"
export USERNAME ENV PATH
[root@atreides sevinsky]# exit
[sevinsky@atreides sevinsky]$ more .bashrc
# .bashrc

# User specific aliases and functions

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi
export
PYHTONPATH=$PATH:/usr/local/reportlab:/usr/local/Numeric-22.0:/usr/local/
egenix-mx-base-2.0.4:/usr/local/biopython-1.10
[sevinsky@atreides sevinsky]$`


Any help would be appreciated.  I have had this problem on both Mandrake
9.0 (the text you saw).  I also tried installing on Redhat 8.0 and as root
I got the same error.

Thanks,
Joel

*******************************************
Joel Sevinsky, Ph.D.
Department of Biochemistry
Campus Box 215
University of Colorado
Boulder, CO  80309

(303)492-7794     FAX: (303)492-2439
joel@sevinsky.com
http://www.sevinsky.com
******************************************