[BioPython] Uniprot Parser

[Ruchira Datta]

I've been using Bio.SwissProt.SProt to parse this file.  The only glitch
that came up so far is that when some fields span multiple lines (e.g., OS,
the species field), SProt puts a newline in the field.  This is not
correct--it should be just a blank space.  However, this can easily be
corrected within SProt itself without requiring a forked parser.

At least two other parsers for this file have been written by people in my
group, but I have pushed and implemented standardization on the BioPython
one.  Part of the point of BioPython is to have one central repository for
development and maintenance of things like this, so that hundreds of people
don't have to spend their time reinventing the wheel.  It is much preferable
that people contribute changes rather than creating a forked version.

--Ruchira

On Sat, Feb 23, 2008 at 2:00 PM, João Rodrigues <anaryin at gmail.com> wrote:

> Hello all!
>
> I've written a small parser for the uniprot_sprot.dat files that come out
> once and again because I read about some incompatibilities of the
> Biopython's with the source files. Now I want to rewrite and clean the
> code
> and I'm considering (strongly) to rewrite my parser. It's a mess of a code
> (though it works) and I'd rather use something more... readable! So, I'm
> asking, basically, is Biopython's parser good already or are there still
> some incompatibilities?
>
> Thanks a lot!
>
> João Rodrigues
>
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