[BioPython] script to extract records from nucleotide database

[Matthew Abravanel]

Hi everyone,

Thanks for all the comments, so since you said you removed Bio.FormatIO in
version 1.44 and replaced it with Bio.SeqIO do you think I can still
successfully use that code I was given if I have 1.44 provided I watch out
for bugs and so on? What is the difference between Bio.FormatIO and
Bio.SeqIO, other then them describing file formats differently? Also how
exactly could one have a partial installation, some of the package not
installing? Thanks again for the help.

Sincerely,

                   Matthew

On Nov 14, 2007 2:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> Iddo Friedberg wrote:
> > The culprit code in Bio/FormatIO ...
>
> We've removed Bio.FormatIO for Biopython 1.44 (in favour of Bio.SeqIO).
> It was a input/output framework based on Martel "regular expressions" to
> describe file formats.
>
> > 1) Can I have the offending code that started all this? (I'm a bit late
> in
> > the game, I know)
>
> I think it was an innocent looking "from Bio import GenBank", which I
> have never seen cause this error before. Hence my wondering if there was
> an installation problem (e.g. a partial installation).
>
> > 2) What is (was) Bio.formats? has it been replaced by something else?
> > 3) What is this registry thingy? We need it?
>
> I think Bio.formats and the registry thing are all tied together with
> code in Bio/formatdefs,  Bio/config etc.  Its all very complicated, and
> doesn't seem to be much documented.
>
> Peter
>
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