[Biopython-dev] FormatIO and SwissProt

[Jeffrey Chang]

On Thursday, July 3, 2003, at 02:43  AM, Yves Bastide wrote:

> Jeffrey Chang wrote:
>> On Wednesday, July 2, 2003, at 10:03  AM, Yves Bastide wrote:
[SwissProt in FormatIO fails on SwissProt file]

>> And yes, you've hit the problem right on the nose.  There are two  
>> Swiss-Prot parsers.  The FormatIO one is still considered 
>> experimental,  and is not maintained as well.  I'd recommend using 
>> the  Bio/SwissProt/SProt parser instead.
>
> There are three SP parsers: Bio/SwissProt/SProt and two for FormatIO 
> (../Bio/expressions/swissprot/sprot{38,40}.py)
>
> I'd like to use FormatIO because
>
> 1. It's cool to use the same code whether I'm accessing nr or sprot or 
> something else
>
> 2. Bio.SeqRecord: to insert into a database.  One can't get a 
> Bio.SeqRecord from SProt, I think

Yes, both are excellent points.  Andrew started the framework for 
Bio.expressions and started to populate it with some parsers.  However, 
he soon got busy with other things (like EUtils).  We really need 
someone to pick up work on this (hint, hint :), before we can really 
start pushing it for mainstream use.


> About GenBank:
> GenBank.FeatureParser uses a nice Martel parser, FormatIO an 
> experimental-unmaintened one; couldn't FormatIO use the good one? 
> (OTOH Bio.SwissProt.SProt is not Martel-based)

Yes, this has been discussed before.  Someone needs to migrate the 
code, which will require some work, I think.

The Bio.SwissProt.SProt parser pre-dates Martel.

Jeff