Biopython 1.74 released

Posted on July 16, 2019 by Peter

Dear Biopythoneers,

Biopython 1.74 has been released and is available from our website and PyPI.

This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

(Please note we will be dropping support for Python 2.7 in early 2020.)

Over half 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.

Our core sequence objects (Seq, UnknownSeq, and MutableSeq) now have a string-like .join() method.

The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning the fields may not always follow the historical column based positions. We no longer give a warning when parsing these. We now allow writing such files (although with a warning as support for reading them is not yet widespread).

Support for the mysqlclient package, a fork of MySQLdb, has been added.

We now capture the IDcode field from PDB Header records.

Bio.pairwise2‘s pretty-print output from format_alignment has been optimized for local alignments: If they do not consist of the whole sequences, only the aligned section of the sequences are shown, together with the start positions of the sequences (in 1-based notation). Alignments of lists will now also be prettily printed.

Bio.SearchIO now supports parsing the text output of the HHsuite protein sequence search tool. The format name is hhsuite2-text and hhsuite3-text, for versions 2 and 3 of HHsuite, respectively.

Bio.SearchIO HSP objects has a new attribute called output_index. This attribute is meant for capturing the order by which the HSP were output in the parsed file and is set with a default value of -1 for all HSP objects. It is also used for sorting the output of QueryResult.hsps.

Bio.SeqIO.AbiIO has been updated to preserve bytes value when parsing. The goal of this change is make the parser more robust by being able to extract string-values that are not utf-8-encoded. This affects all tag values, except for ID and description values, where they need to be extracted as strings to conform to the SeqRecord interface. In this case, the parser will attempt to decode using utf-8 and fall back to the system encoding if that fails. This change affects Python 3 only.

Bio.motifs.mast has been updated to parse XML output files from MAST over the plain-text output file. The goal of this change is to parse a more structured data source with minimal loss of functionality upon future MAST releases. Class structure remains the same plus an additional attribute Record.strand_handling required for diagram parsing.

Bio.Entrez now automatically retries HTTP requests on failure. The maximum number of tries and the sleep between them can be configured by changing Bio.Entrez.max_tries and Bio.Entrez.sleep_between_tries. (The defaults are 3 tries and 15 seconds, respectively.)

All tests using the older print-and-compare approach have been replaced by unit tests following Python’s standard testing framework.

On the documentation side, all the public modules, classes, methods and functions now have docstrings (built in help strings). In addition to displaying the Biopython API documentation via epydoc, we now also have the Biopython API documentation via Sphinx (which we hope to make the default in future). Furthermore, the PDF version of the Biopython Tutorial and Cookbook now uses syntax coloring for code snippets.

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:

• Andrey Raspopov (first contribution)
• Antony Lee
• Benjamin Rowell (first contribution)
• Bernhard Thiel
• Brandon Invergo
• Catherine Lesuisse
• Chris Rands
• Deepak Khatri (first contribution)
• Gert Hulselmans
• Jared Andrews
• Jens Thomas (first contribution)
• Konstantin Vdovkin
• Lenna Peterson
• Mark Amery
• Markus Piotrowski
• Micky Yun Chan (first contribution)
• Nick Negretti
• Peter Cock
• Peter Kerpedjiev
• Ralf Stephan
• Rob Miller
• Sergio Valqui
• Victor Lin
• Wibowo ‘Bow’ Arindrarto
• Zheng Ruan

For reference, checksums:

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