[BioPython] script to extract records from nucleotide database

[Iddo Friedberg]

The culprit code in Bio/FormatIO

class FormatIO:
    def __init__(self, name,
                 default_input_format = None,
                 default_output_format = None,
                 abbrev = None,
                 registery = None):
        if abbrev is None:
            abbrev = name
        if registery is None:
            import Bio
            registery = Bio.formats


seems like this class is being instantiated from SeqRecord.py using the
following call:

io = FormatIO.FormatIO("SeqRecord",
                         default_input_format = "sequence",
                         default_output_format = "fasta")


Which causes 'registry' to be set to None, which causes  a call to
Bio.formats which does not exist.

1) Can I have the offending code that started all this? (I'm a bit late in
the game, I know)
2) What is (was) Bio.formats? has it been replaced by something else?
3) What is this registry thingy? We need it?

Iddo





On Nov 14, 2007 1:47 AM, Christof Winter <winter at biotec.tu-dresden.de>
wrote:

> Peter wrote:
> > Matthew Abravanel wrote:
> >> Hi Christof and everyone,
> >>
> >> Thanks for all the comments and everything, the OS I am using is NetBSD
> >> 3.1 , and I think you were right Peter about my biopython version I
> think it
> >> was 1.43 instead of the latest 1.44 version.  If I get the latest
> >> 1.44v ersion  of biopython do you think the code should work or do I
> >> need to think of something else?
> >
> > Well, that example code looked like it should have worked on Biopython
> > 1.43 so I am a little puzzled.
>
> I even run 1.42 (Debian package python-biopython 1.42-2), and it works
> fine.
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 

I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."