[BioPython] interbase vs one-based?

[Ann Loraine]

Hello,

I'm not sure if this is a bug or not...my apologies if this has
already been discussed.

I parsed a Genbank file using BioPython and got this:

>>> f = rec.features[1]
>>> print f
type: gene
location: [221:1607]
ref: None:None
strand: 1
qualifiers:
        Key: db_xref, Value: ['GeneID:911526']
        Key: locus_tag, Value: ['MYPU_0010']
        Key: note, Value: ['dnaA']

Note the coordinates - the feature's start position is 221 and end
position is 1607, seemingly.

However, the text of the Genbank file for this feature says this:

     gene          222..1607
                     /locus_tag="MYPU_0010"
                     /note="dnaA"
                     /db_xref="GeneID:911526"

It looks like the Genbank parser converts coordinates from 1-based to
interbase coordinates. Is this correct?

Yours,

Ann

-- 
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