Biopython 1.69 released

Great news for all bioinformatitians out there  – new biopython version was released.

What is new?

First of all Python 2.6 was dropped for further development, but many other versions are supported (Python 2.7, 3.3, 3.4, 3.5, 3.6, PyPy v5.7, PyPy3.5 v5.7 beta, and Jython 2.7).

Many changes has been made, both improving performance and functionality, broadening compatibilities with biological databases.

  • Bio.AlignIO supports MAF format,
  • Bio.SearchIO.AbiIO support FSA files,
  • Uniprot parser parse “submittedName” in XML files,
  • NEXUS parser was improved to improve co-working with tools like the BEAST TreeAnnotator,
  • New parser was introduced for ExPASy Cellosaurus,
  • Bio.Seq module has complement function,
  • SeqFeature object’s qualifiers is explicitly ordered dictionary,
  • Bio.SeqIO UniProt-XML parser was updated to cope with features with unknown locations which can be found in mass spec data.
  • Bio.SeqIO GenBank, EMBL, and IMGT parsers were updated,
  • Bio.Affy package supports CEL format version 4,
  • Bio.Restriction enzyme list has been updated,
  • Bio.PDB.PDBList now can download PDBx/mmCif (new default).

What I really like is that they use “Python PEP8, PEP257 and best practice standard coding style”. Great example to others ;).

You can check out all contributors and details here:

Maybe some day you (or I) will be at this list?

And… have fun with new Biopython 🙂


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