[BioPython] genbank parser returns start position of the location decreased by one

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Mon Oct 17 08:24:23 EDT 2005


Hi Michiel,
  I thought this might be the "feature" of this, but imagine you just parse
genbank data and display on the web web. I don't believe anybode would expect
that the data fetched through biopython differ from those visible on the NCBI
web. Is this "feature" at least consistent with bioperl's behavior?
M.

Michiel De Hoon wrote:
> I would think that this is intentional. Python uses zero-based arrays,
> Genbank starts counting at 1.
> In other words, gb_seqrecord.seq[0:4115] will return the sequence that you're
> interested in.


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