[Biopython-announce] Biopython 1.49 beta released

Peter biopython at maubp.freeserve.co.uk
Sun Nov 9 15:16:50 UTC 2008

Dear Biopythoneers,

We are pleased to announce a beta release of Biopython 1.49. There are
been some significant changes since Biopython 1.48 was released two
months ago, which is why we are initially releasing a beta for wider

As previously announced, the big news is that Biopython now uses NumPy
rather than its precursor Numeric (the original Numerical Python

As in the previous releases, Biopython 1.49 beta supports Python 2.3,
2.4 and 2.5 but should now also work fine on Python 2.6. Please note
that we intend to drop support for Python 2.3 in a couple of releases

We also have some new functionality, starting with the basic sequence
object (the Seq class) which now has more methods. This encourages a
more object orientated coding style, and makes basic biological
operations like transcription and translation more accessible and

Our BioSQL interface can now optionally fetch the NCBI taxonomy on
demand when loading sequences (via Bio.Entrez) allowing you to
populate the taxon/taxon_name tables gradually. Also, BioSQL should
now work with the psycopg2 driver for PostgreSQL (as well as the older
psycopg driver).

Finally, our old parsing infrastructure (Martel and Bio.Mindy) is now
considered to be deprecated, meaning mxTextTools is no longer required
to use Biopython. This should not affect any of the typically used
parsers (e.g. Bio.SeqIO and Bio.AlignIO).

So, if you are feeling brave and know the risks, please try out
Biopython 1.49 beta, and let us know on the mailing lists if it works,
or more importantly if something doesn't.

We'd also like feedback on the updated Biopython Tutorial and Cookbook:

Source distributions and Windows installers are available from the
Biopython website:


-Peter on behalf of the Biopython developers

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