[BioPython] installation help

[Sevinsky Joel]

OK, I am learning a bit here.  It seems I did not understand how the
interpreter works, and thought that when I called a module a second time
and there was no error that it imported correctly.  Wrong.  Anyway, while
trying to do anything I can think of, I started adding the mx
subdirectories explicitly to my PYTHONPATH, all the way down to
/usr/local/egenix-mx-base-2.0.4/mx/TextTools/mxTexttools,  and this is the
latest set of errors:

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 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 ?
  File "/usr/local/egenix-mx-base-2.0.4/mx/TextTools/__init__.py", line 8,
in ?
    from TextTools import *
  File "/usr/local/egenix-mx-base-2.0.4/mx/TextTools/TextTools.py", line
13, in ?
    from mxTextTools import *
  File
"/usr/local/egenix-mx-base-2.0.4/mx/TextTools/mxTextTools/__init__.py",
line 9, in ?
    from mxTextTools import __version__
ImportError: cannot import name __version__
>>>

Any help would be appreciated.

Joel



On Mon, 13 Jan 2003, Sevinsky  Joel wrote:

> Andrew,
>
> So I am rather new to this but the following seems pretty strange.  I
> looked at importing Martel and this is what I got:
>
> [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 Martel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   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
> >>> 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 35, in ?
>     from Bio import StdHandler
>   File "/usr/local/biopython-1.10/Bio/StdHandler.py", line 5, in ?
>     from Bio import Std, Decode
>   File "/usr/local/biopython-1.10/Bio/Std.py", line 4, in ?
>     Group = Martel.Group
> AttributeError: 'module' object has no attribute 'Group'
> >>> import Martel
> >>> import Bio
> >>>
>
> First they both fail, and then they both work.  import Martel comes up
> with the same TextTools error, then Bio has a new error, and then they
> both import fine.
>
> Joel
>
>
> On Mon, 13 Jan 2003, Andrew Dalke wrote:
>
> > Joel Sevinsky:
> > > Yes, the typo was the cause of the mxBASE not loading, but I still have the
> > > Bio problem.  After I corrected the typo both root and sevinsky have the
> > > same problem as I reported for root earlier.  Thanks.
> >
> >
> >   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
> > >>>
> >
> > I was going to say you need to install mxTextTools as well as
> > mxBASE.  However, I see that you have a very strange exception.
> > How did a reportlab file get stuck in the traceback.
> >
> > Can you 'import Martel' by itself?
> >
> > 					Andrew
> > 					dalke@dalkescientific.com
> > _______________________________________________
> > BioPython mailing list  -  BioPython@biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> >
>
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