Biopython 1.73 released

Dear Biopythoneers,

Biopython 1.73 has been released and is available from our website and PyPI.

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”.  See the LICENSE.rst file for more details.

The dictionary-like indexing in Bio.SeqIO and Bio.SearchIO will now explicitly preserve record order to match a behaviour change in the Python standard dict object. This means looping over the index will load the records in the on-disk order, which will be much faster (previously it would be effectively at random, based on the key hash sorting).

The “grant” matrix in Bio.SubsMat.MatrixInfo has been replaced as our original values taken from Gerhard Vogt’s old webpages at EMBL Heidelberg were discovered to be in error. The new values have been transformed following Vogt’s approach, taking the global maximum 215 minus the similarity scores from the original paper Grantham (1974), to give a distance measure.

Double-quote characters in GenBank feature qualifier values in Bio.SeqIO are now escaped as per the NCBI standard. Improperly escaped values trigger a warning on parsing.

There is a new command line wrapper for the BWA-MEM sequence mapper.

The string-based FASTA parsers in Bio.SeqIO.FastaIO have been optimised, which also speeds up parsing FASTA files using Bio.SeqIO.parse().

Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Alona Levy-Jurgenson (first contribution)
  • Ariel Aptekmann
  • Brandon Invergo
  • Catherine Lesuisse
  • Chris Rands
  • Darcy Mason (first contribution)
  • Devang Thakkar (first contribution)
  • Ivan Antonov (first contribution)
  • Jeremy LaBarage (first contribution)
  • Juraj Szász (first contribution)
  • Kai Blin
  • Konstantin Vdovkin (first contribution)
  • Manuel Nuno Melo (first contribution)
  • Maximilian Greil
  • Nick Negretti (first contribution)
  • Peter Cock
  • Rona Costello (first contribution)
  • Spencer Bliven
  • Wibowo ‘Bow’ Arindrarto
  • Yi Hsiao (first contribution)

For reference, checksums:

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$ sha256sum biopython-1.73*
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