[Biopython-dev] Something wrong with Martel?

Jeffrey Chang jefftc at stanford.edu
Sat Jul 26 13:22:13 EDT 2003

Thanks for that patch!  I've committed it, and the LAX test suite runs 
properly now.


On Friday, July 25, 2003, at 01:29  AM, Andreas Kuntzagk 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?
> 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
> <LAX.py.diff>_______________________________________________
> Biopython-dev mailing list
> Biopython-dev at biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

More information about the Biopython-dev mailing list