[Biopython-dev] Python 3 and Bio.SeqIO.index()

Peter biopython at maubp.freeserve.co.uk
Mon Jan 17 18:04:27 UTC 2011

Continuing a thread back in July 2010,

On Thu, Jul 15, 2010 at 2:31 PM, Peter wrote:
> I think the clear message (from both Windows and Linux) is that for
> Bio.SeqIO.index() to perform at a tolerable speed on Python 3 we
> can't use the default text mode with unicode strings, we are going
> to have to use binary mode with bytes.

I've now done that - which brings the time for test_SeqIO_index.py
down for Python 3.x to roughly the same as Python 2.x (about a
four fold speed up).

Under Windows there may also be a slight speed up for Python 2,
while on Linux/Mac there could be a slight slow down. I expect we
can work on this.

The good news is this yet another step towards supporting
Biopython under Python 3.


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