[Biopython-dev] 1.57 release plans

[Eric Talevich]

On Fri, Apr 1, 2011 at 2:50 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> 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.
>
>
The Bio.PDB module received several fixes and improvements. We've started
merging João's work from GSoC 2010, and consequently Atom objects now know
their element type and IUPAC mass. (The new features that use these
attributes won't be included in Biopython until the next release, though, so
stay tuned.)

-E