[Biopython] pro

[Björn Johansson]

Hi,
thank you very much for the information, I think it has to do with the
docstrings, if I run with python -OO under linux, I get the same error msg.

as for the two spark files, they seem identical, spark.py is the one i
downloaded from
http://biopython.org/SRC/biopython/Bio/Parsers/spark.py:

diff -w spark.py /usr/local/lib/python2.6/dist-packages/Bio/Parsers/spark.py

produces no output at all.

I will try and find out if the optimization can be overridden for one file
only.

Thanks!
/bjorn


2010/4/5 Peter Cock <p.j.a.cock at googlemail.com>

> 2010/4/5 Eric Talevich <eric.talevich at gmail.com>
> >
> > It looks like spark relies on the docstrings in
> Bio.GenBank.LocationParser.
> > Is there anything in py2exe that would strip the docstrings from compiled
> > modules? Some optimizations do this -- I think "python -O3" strips
> > docstrings, for instance.
>
> You may be on to something there Eric.
>
> Björn, could compare your file:
> z:/usr/local/lib/python2.6/dist-packages\Bio\Parsers\spark.py
> with the version we provide:
> http://github.com/biopython/biopython/blob/master/Bio/Parsers/spark.py
> or:
> http://biopython.org/SRC/biopython/Bio/Parsers/spark.py
>
> In the medium term, I'd like to move the GenBank/EMBL location
> parsing to something simpler and faster (using regular expressions)
> and then deprecate Bio.GenBank.LocationParser and indeed the
> whole of Bio.parsers (which just has a copy of spark). There is
> a bug open on this with some code. But that isn't going to help
> Björn right now.
>
> Peter
>



-- 
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Björn Johansson
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