[BioPython] Martel Parser error...
Peter
biopython at maubp.freeserve.co.uk
Tue Jul 10 19:27:15 UTC 2007
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
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