Biopython 1.69 released
This release of Biopython supports Python 2.7, 3.3, 3.4, 3.5 and 3.6 (we have now dropped support for Python 2.6). It has also been tested on PyPy v5.7, PyPy3.5 v5.7 beta, and Jython 2.7.
We have started to dual-license Biopython under both our original liberal “Biopython License Agreement”, and the very similar but more commonly used “3-Clause BSD License”. In this release a small number of the Python files are explicitly available under either license, but most of the code remains under the “Biopython License Agreement” only. See the LICENSE file for more details.
We now expect and take advantage of NumPy under PyPy, and compile most of the Biopython C code modules as well.
Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the format name “maf”, using new module Bio.AlignIO.MafIO which also offers indexed access to these potentially large files using SQLite3 (contributed by Andrew Sczesnak, with additional refinements from Adam Novak).
Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The underlying format (ABIF) remains the same as AB1 files and so the string ‘abif’ is the expected format argument in the main SeqIO functions. AbiIO determines whether the file is AB1 or FSA based on the presence of specific tags.
The Uniprot parser is now able to parse “submittedName” elements in XML files.
The NEXUS parser handling of internal node comments has been improved, which should help if working with tools like the BEAST TreeAnnotator. Slashes are now also allowed in identifiers.
New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue, and cell line ontology (contributed by Steve Marshall).
For consistency the Bio.Seq module now offers a complement function (already available as a method on the Seq and MutableSeq objects).
The SeqFeature object’s qualifiers is now an explicitly ordered dictionary (note that as of Python 3.6 the Python dict is ordered by default anyway). This helps reproduce GenBank/EMBL files on input/output.
The Bio.SeqIO UniProt-XML parser was updated to cope with features with unknown locations which can be found in mass spec data.
The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type from the LOCUS/ID line explicitly in the record.annotations dictionary. The Bio.SeqIO EMBL parser was updated to cope with more variants seen in patent data files, and the related IMGT parser was updated to cope with IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed. The GenBank output now uses colon space to match current NCBI DBLINK lines.
The Bio.Affy package supports Affymetrix version 4 of the CEL file format, in addition to version 3.
The restriction enzyme list in Bio.Restriction has been updated to the February 2017 release of REBASE.
Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default), PDBML/XML and mmtf format protein structures. This is inline with the RCSB recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython already has support for parsing mmCif files.
Additionally, a number of small bugs 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:
- Aaron Rosenfeld
- Adam Kurkiewicz (first contribution)
- Adam Novak (first contribution)
- Adrian Altenhoff (first contribution)
- Allis Tauri (first contribution)
- Andrew Dalke
- Andrew Guy (first contribution)
- Andrew Sczesnak (first contribution)
- Ben Fulton
- Bernhard Thiel (first contribution)
- Bertrand Néron
- Blaise Li (first contribution)
- Brandon Carter (first contribution)
- Brandon Invergo
- Carlos Pena
- Carlos Ríos
- Chris Warth
- Emmanuel Noutahi
- Foen Peng (first contribution)
- Francesco Gastaldello (first contribution)
- Francisco Pina-Martins (first contribution)
- Hector Martinez (first contribution)
- Jacek Śmietański
- Jack Twilley (first contribution)
- Jeroen Van Goey (first contribution)
- Joshua Meyers (first contribution)
- Kurt Graff (first contribution)
- Lenna Peterson
- Leonhard Heizinger (first contribution)
- Marcin Magnus (first contribution)
- Markus Piotrowski
- Maximilian Greil (first contribution)
- Michał J. Gajda (first contribution)
- Michiel de Hoon
- Milind Luthra (first contribution)
- Oscar G. Garcia (first contribution)
- Owen Solberg
- Peter Cock
- Richard Neher (first contribution)
- Sebastian Bassi
- Sourav Singh (first contribution)
- Spencer Bliven (first contribution)
- Stefans Mezulis
- Steve Bond
- Steve Marshall (first contribution)
- Uri Laserson
- Veronika Berman (first contribution)
- Vincent Davis
- Wibowo ‘Bow’ Arindrarto
Thank you all.
P.S. You can follow @Biopython on Twitter
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