[BioPython] Parsing GenBank and Swiss-Prot with FormatIO

[Jeffrey Chang]

Right now, you can use FormatIO to read files into SeqRecord objects 
(although that is extensible).
from Bio import SeqRecord
sequence_iterator = SeqRecord.io.readFile(open("MYSEQUENCEFILE"))
first_seq = sequence_iterator.next()

Currently, Biopython only supports FASTA, SWISS-PROT, Genbank, and EMBL 
formats for MYSEQUENCEFILE.  However, it can technically handle any 
format with a Martel definition under Bio/expressions.  The expressions 
are not as well tested as the standard parsers, so it may not be able 
to handle exceptional records as well.  To read files, do something 
like:

Jeff


On Wednesday, March 12, 2003, at 01:28 PM, Yves Bastide wrote:

> Hi,
>
> A quick, basic question I can't find the answer right now: How to use 
> FormatIO?
>
> Thanks,
>
> yves
>
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython