[BioPython] Martel Parser error...

[Peter]

Michael Mayhew wrote:
> Greetings,
> 
>   I am using BioPython-1.42 (also tried 1.43) on Mac OS X (10.4.8) and 
> have successfully compiled/installed the prerequisite packages (Numeric 
> and mxTextTools).
> 
>   I have been receiving a Martel Parser error as detailed in the 
> following readout (from a python interactive session), when I try to use 
> either Fasta.RecordParser() or Fasta.SequenceParser() instances:
> 
>       >>tester = iter.next()
>        Traceback (most recent call last):
 > ...

Could you give a complete stand alone example? I'm not sure what you are 
trying to do here...

Have you looked at Bio.SeqIO (available in Biopython 1.43) instead of 
Bio.Fasta?

http://biopython.org/wiki/SeqIO

>   I confirmed this when I ran the included test suites (with python 
> setup.py test).

Could you show us the failed test result?

>   I have seen some suggestions to get the most recent CVS version of 
> biopython to rectify this problem. How would I go about this?
> 
>   Is getting the most recent CVS version of biopython the only/best 
> thing to do?

I'm not sure what's wrong here - so its hard to say if CVS would be any 
better. I've not used Biopython on Mac OS X, but it should work.

Peter