[Biopython-dev] Something wrong with Martel?

[Yair Benita]

on 25/7/2003 10:29, Andreas Kuntzagk at andreas.kuntzagk at mdc-berlin.de
wrote:

> Hi,
> 
>> Andreas, this looks like it might be related to the switch over to
>> using a dict object?  Could you take a look at it?
> 
> First issue is related to dict. Appended a diff to patch this.
> 
> Would be good if setup.py in BioPython root dir would also test the
> Martel tests.
> 
>>> Second, trying to run the same script as Andrew wrote in the Readme
>>> (attached), I only get:
>>> <?xml version="1.0" encoding="iso-8859-1"?>
>>> 
>>> Basically nothing is executed after the command:
>>> parser.parse(open(File))
>>> 
>>> Is something wrong on my system or something wrong with the Martel
>>> code?
>>> Could anyone try to run the above script?
> Yair, do you have a file "/etc/passwd" (looks like your email is from a
> Windows system)? What do you mean "nothing is executed"? Script hangs,
> script returns whithout output, script throws an error?
> 
I do have the file, I work on Mac OS X.
The script just terminates after the command parser.parse and all the
commands after that are not executed. There is no error to suggest that
something went wrong.

> The parser.parse works for me, but the script is failing at
> doc.normalize() whith
> 
> AttributeError: 'NoneType' object has no attribute 'normalize'
> 
> I still don't know enough about the Martel infrastructure to understand
> this. sax2dom.document seems to be None.
> 
> By, Andreas
> 

Greg Tyrelle solved the problem for me (see following email), but still I
find it strange that Martel does not raise an error when the format is not
matching the file being parsed.

Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University