[BioPython] Martel not installed in MacOSX biopython distribution ?

[Brad Chapman]

Hi Catherine;

> We have a recent biopython installation (biopython-1.24.tar.gz) on a MacOsX platform.
> 
> When using the parse function from module Bio.Clustalw, we get an error message saying 
> that Martel is missing. Otherwise, all the biopython modules work well.
> Also, when pointing to the Martel link (http://www.biopython.org/~dalke/Martel/
> and http://www.bioinformatics.org/bradstuff/bp/api/Martel/index.html), we
> get a 'not found' message.
> 
> Is there a known problem of Martel module missing when installing biopython?

Yes, I did clean up some bad code I wrote a while back in the
Clustalw module -- as of revision 1.8 of
Bio/Clustalw/clustaw_format.py in CVS (since March). I had an import
check there from way back in the days when Martel was distributed
separately from Biopython, hence the bad URL as well. So this should
behave better in future releases -- sorry for the confusion with
that.

As to the symptoms of your problems, Martel should be installed by 
default with Biopython -- you can check this using:

>>> import Martel

at a python prompt. If all other Biopython modules are working and
Clustalw is not, then it is very likely that Martel is installed but
something else may be the problem.

So I guess the best way to proceed and check out the problem is:

1. Does 'import Martel' work? If not, what kind of error message are
you getting? The only current known problems with 1.24 and Martel
installation are that it can be a little strange if there is an old
Martel instance already installed into site-packages. This should be
fixed in the next release, but the quick fix is to remove
site-packages/Martel and install again.

2. Try and get the latest changes in Clustalw/clustal_format.py and
install this in place of the 1.24 version. Hopefully then you should
at least see the problem with the import Martel call and we can
diagnose the problem further.

I hope this helps. Sorry about any problems and be sure to write
again if this doesn't clear things up.

Brad