[Biopython-dev] parsers status

[Jeffrey Chang]

The FormatIO system is starting to mature, so it is a good idea to 
start thinking about using Martel expressions for new parsers (and 
possibly porting old ones).  The new system has a lot of advantages, 
such as exporting a unified interface, format auto-detecting, 
integration with data loading.

I've gone through and taken an inventory of the current Biopython 
parsers.  The ones under the PARSERS heading are the parsers that are 
not integrated with FormatIO, and EXPRESSIONS are the ones that are.  I 
am sorry if I have missed any -- it is unintentional and not indicative 
of any negative opinion of your code!

The eventual goal is to get all of them under the EXPRESSIONS heading.  
The Martel-based parsers will be easier to do than the non-Martel ones. 
  I imagine that there will be a slow migration path; new parsers will 
be developed with FormatIO in mind, and old ones will be ported over as 
needed.

Jeff



PARSERS
Blast.NCBIStandalone
Blast.NCBIWWW
Clustalw                     (Martel)
Emboss.primer3_format        (Martel)
Emboss.primersearch_format   (Martel)
Enzyme
FSSP
Fasta
GenBank           (Martel)
Geo               (Martel)
Gobase
Intelligenetics   (Martel)
KEGG.Enzyme       (Martel)
KEGG.Compound     (Martel)
KEGG.Map          (Martel)
Kabat             (Martel)
LocusLink         (Martel)
Medline           (Martel)
MetaTool          (Martel)
NBRF              (Martel)
PDB
Prosite
Rebase
SCOP
Saf               (Martel)
SwissProt
UniGene


EXPRESSIONS
blocks
fasta
sprot38
sprot40
genbank
embl65
ncbiblast
wublast