[Biopython-dev] SearchIO HSP indexing

Peter Cock p.j.a.cock at googlemail.com
Sat Feb 9 15:36:34 UTC 2013

> Am 2013-02-09 15:30, schrieb Peter Cock:
>> One reason for this is to be consistent across all the formats supported
>> in SearchIO, and since Biopython is a Python library following Python
>> norms seems most natural.

On Sat, Feb 9, 2013 at 3:12 PM, Markus Piotrowski
<Markus.Piotrowski at ruhr-uni-bochum.de> wrote:
> Mmh, at least Bio.Blast.NCBIXML returns the exact values given in the xml
> result.

Yes, the old Bio.Blast parsers do not try and convert the co-ordinates.
Given they were only handling BLAST output that was a justifiable
option. With Bio.SearchIO we're not just modelling BLAST output
though - it covers multiple formats with different conventions.


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