Biopython 1.72 released

Dear Biopythoneers,

I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:

https://biopython.org/wiki/Download
https://pypi.python.org/pypi/biopython/1.72

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.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).

The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use inclusive end co-ordinates to better handle searches at end points. This will require you to rebuild any existing MAF index files.

In this release 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 Entrez module now supports the NCBI API key. Also you can now set a custom directory for DTD and XSD files. This allows Entrez to be used in environments like AWS Lambda, which restricts write access to specific directories. Improved support for parsing NCBI Entrez XML files that use XSD schemas.

Internal changes to our C code mean that NumPy is no longer required at compile time – only at run time (and only for those modules which use NumPy).

Seq, UnknownSeq, MutableSeq and derived classes now support integer multiplication methods, matching native Python string methods.

A translate method has been added to Bio.SeqFeature that will extract a feature and translate it using the codon_start and transl_table qualifiers of the feature if they are present.

Bio.SearchIO is no longer considered experimental, and so it does not raise warnings anymore when imported.

A new pairwise sequence aligner is available in Bio.Align, as an alternative to the existing pairwise sequence aligner in Bio.pairwise2.

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

  • Benjamin Vaisvil (first contribution)
  • Blaise Li
  • Chad Parmet
  • Chris Rands
  • Connor T. Skennerton
  • Francesco Gastaldello
  • Michiel de Hoon
  • Pamela Russell (first contribution)
  • Peter Cock
  • Spencer Bliven
  • Wibowo ‘Bow’ Arindrarto

Thank you all.

Peter

P.S. You can follow @Biopython on Twitter

Checksums for interest/public record:

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biopython-1.72-cp34-cp34m-win_amd64.whl

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biopython-1.72-cp35-cp35m-win_amd64.whl

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biopython-1.72-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

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biopython-1.72-cp36-cp36m-manylinux1_i686.whl

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biopython-1.72-cp36-cp36m-win_amd64.whl

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biopython-1.72.tar.gz

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biopython-1.72.zip
$ md5sum biopython-1.72*

661d50514eaa8151192b2127f52a8f5e
biopython-1.72-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

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biopython-1.72-cp27-cp27m-manylinux1_x86_64.whl

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biopython-1.72-cp27-cp27mu-manylinux1_x86_64.whl

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biopython-1.72-cp35-cp35m-manylinux1_x86_64.whl

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f043fa59e3fbd5d505599474aaed74b5  biopython-1.72-cp35-cp35m-win_amd64.whl

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49fd975593798f0d7a293ebe327f800e  biopython-1.72-cp36-cp36m-manylinux1_i686.whl

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biopython-1.72-cp36-cp36m-manylinux1_x86_64.whl

4e0d4de83b89d632a5dad9ee417306f2  biopython-1.72-cp36-cp36m-win32.whl

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