[Biopython-dev] Something wrong with Martel?

Andreas Kuntzagk andreas.kuntzagk at mdc-berlin.de
Fri Jul 25 04:30:37 EDT 2003


> 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
-------------- next part --------------
Index: LAX.py
RCS file: /home/repository/biopython/biopython/Martel/LAX.py,v
retrieving revision 1.3
diff -r1.3 LAX.py
<         self.data.clear()
>         self.clear()
<         self.data.setdefault(tag, []).append(text)
>         self.setdefault(tag, []).append(text)
<         self.data.setdefault(tag, []).append( (text, attrs) )
>         self.setdefault(tag, []).append( (text, attrs) )
<         self.data.setdefault(tag, []).append(
>         self.setdefault(tag, []).append(

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