[Biopython-dev] Blast parsers and records

Peter biopython at maubp.freeserve.co.uk
Tue Jun 8 12:32:05 UTC 2010

On Tue, Jun 8, 2010 at 1:19 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- On Mon, 6/7/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> I agree that records from all the different BLAST output
>> formats should be represented by a common base class -
>> but not necessarily the same class.
>> For example, the default plain text and XML formats include
>> the pairwise alignments, but the tabular output does not. To
>> me having a sub-class which stores the pairwise alignments seems
>> natural here.
> Why do we need a sub-class? We don't do this in Bio.SeqIO,
> where GenBank files contain much more information than Fasta
> files, but both are represented by a SeqRecord.

OK, I guess you could have some properties which are left empty
(like the annotations dictionary or features list in a SeqRecord
from a FASTA file).


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