[BioPython] interbase vs one-based?

[Ann Loraine]

Thanks!

-Ann

On 12/18/06, Peter (BioPython List) <biopython at maubp.freeserve.co.uk> wrote:
> Ann Loraine wrote:
> > Hello,
> >
> > I'm not sure if this is a bug or not...my apologies if this has
> > already been discussed.
>
> Yes, a raw location of 222..1607 is intentionally converted into a
> location [221:1607] in BioPython.  This has been discussed before on the
> mailing list... but never mind.
>
> The rational is to follow the python string splicing conventions, thus
> req.seq[221:1607] should give you the nucleotides for this feature.
>
> Try:
>
> help(Bio.SeqFeature.FeatureLocation)
>
> or:
>
> print rec.features[1].location.__doc__
>
> You should get something like this:
> > Specify the location of a feature along a sequence.
> >
> > This attempts to deal with fuzziness of position ends, but also make
> > it easy to get the start and end in the 'normal' case (no fuzziness).
> >
> > You should access the start and end attributes with
> > your_location.start and your_location.end. If the start and end are
> > exact, this will return the positions, if not, we'll return the
> > approriate Fuzzy class with info about the position and fuzziness.
> >
> > Note that the start and end location numbering follow Python's
> > scheme, thus a GenBank entry of 123..150 (one based counting) becomes
> > a location of [122:150] (zero based counting).
>
> Peter
>
>


-- 
Ann Loraine
Assistant Professor
Departments of Genetics, Biostatistics, and
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org