[Biopython-dev] 1.57 release plans

[Brad Chapman]

Peter;
Thanks for fixing the BLAST+ issue and the tutorial. We'll plan for
a release later this evening or tomorrow morning, so everyone please
hold off commits until it's finished.

Below are the release notes and contributors list for the release.
Please let me know anything or anyone is missing; additionally if
anyone wants to clean up the text or add more flourishes of
brilliance, that would be very welcome.

Thanks everyone for all the hard work for the release,
Brad


In progress: Biopython 1.57 (not yet released).

Bio.SeqIO now includes an index_db() function which extends the existing
indexing functionality to allow indexing many files, and more importantly
this keeps the index on disk in a simple SQLite3 database rather than in
memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter
tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
ability to run the BLAST tools and save the output as ASN.1 format, and then
convert this to any other supported BLAST ouput format (plain text, tabular,
XML, or HTML) with the blast_formatter tool. The wrappers were also updated
to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The SeqRecord object now has a reverse_complement method (similar to that of
the Seq object). This is most useful to reversing per-letter-annotation (such
as quality scores from FASTQ) or features (such as annotation from GenBank).

Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now
uses an optimised routine for FASTQ to QUAL making this much faster.

Biopython can now be installed with pip. Thanks to David Koppstein and 
James Casbon for reporting the problem.

Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and
IMGT output.

The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary
(previously it was a list of key,value tuples) to better match the standard.

(At least) 14 people have contributed to this release, including 5 new people:

Brad Chapman
Eric Talevich
Erick Matsen (first contribution)
Hongbo Zhu
Jeffrey Finkelstein (first contribution)
Joanna & Dominik Kasprzak (first contribution)
Joao Rodrigues
Kristian Rother
Leighton Pritchard
Michiel de Hoon
Peter Cock
Phillip Garland
Walter Gillett (first contribution)