[Biopython-dev] Bio.SeqIO.index extension, Bio.SeqIO.index_many

Peter biopython at maubp.freeserve.co.uk
Sun Jan 2 21:29:52 UTC 2011

On Sat, Jan 1, 2011 at 9:15 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Checked in, but I still need to look at Python 3 support. Even
> plain Bio.SeqIO.index() will need some re-engineering to run
> at acceptable speed on Python 3, so this isn't unexpected.

There was also a UserDict thing to sort out for Python 3 which
isn't taken care of by 2to3, see http://bugs.python.org/issue2876

However, the biggest annoyance of the index_db stuff was my
unit tests on Windows - it turns out repeatedly creating, using,
closing and deleting a file with the same name was a bad idea.
Something was keeping a stale handle to the file as it wasn't
always getting deleted. In the end I just gave in and used a
different temp file for each tests, and it works fine. Weird,
also rather frustrating - but the tests pass now :)

I wonder how SQLite3 support in Jython is coming along...


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