Changelog for python-biopython-1.69-1.2.x86_64.rpm :
Wed May 24 14:00:00 2017 toddrme2178AATTgmail.com
- Implement single-spec version
- Fix source URL.
- updated to version 1.69

* We now expect and take advantage of NumPy under PyPy, and compile most of the
Biopython C code modules as well.

* Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the
format name \"maf\", using new module Bio.AlignIO.MafIO which also offers
indexed access to these potentially large files using SQLite3 (contributed by
Andrew Sczesnak, with additional refinements from Adam Novak).

* Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The
underlying format (ABIF) remains the same as AB1 files and so the string
\'abif\' is the expected format argument in the main SeqIO functions. AbiIO
determines whether the file is AB1 or FSA based on the presence of specific
tags.

* The Uniprot parser is now able to parse \"submittedName\" elements in XML files.

* The NEXUS parser handling of internal node comments has been improved, which
should help if working with tools like the BEAST TreeAnnotator. Slashes are
now also allowed in identifiers.

* New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue,
and cell line ontology (contributed by Steve Marshall).

* For consistency the Bio.Seq module now offers a complement function (already
available as a method on the Seq and MutableSeq objects).

* The SeqFeature object\'s qualifiers is now an explicitly ordered dictionary
(note that as of Python 3.6 the Python dict is ordered by default anyway).
This helps reproduce GenBank/EMBL files on input/output.

* The Bio.SeqIO UniProt-XML parser was updated to cope with features with
unknown locations which can be found in mass spec data.

* The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type
from the LOCUS/ID line explicitly in the record.annotations dictionary.
The Bio.SeqIO EMBL parser was updated to cope with more variants seen in
patent data files, and the related IMGT parser was updated to cope with
IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed.
The GenBank output now uses colon space to match current NCBI DBLINK lines.

* The Bio.Affy package supports Affymetrix version 4 of the CEL file format,
in addition to version 3.

* The restriction enzyme list in Bio.Restriction has been updated to the
February 2017 release of REBASE.

* Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default),
PDBML/XML and mmtf format protein structures. This is inline with the RCSB
recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython
already has support for parsing mmCif files.

* Additionally, a number of small bugs 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.

Thu Nov 17 13:00:00 2016 alinm.elenaAATTgmail.com
- updated to version 1.68

Mon Dec 9 13:00:00 2013 toddrme2178AATTgmail.com
- Update to version 1.63

* 2to3 no longer needed for python 3
- Added additional dependencies

Thu Sep 19 14:00:00 2013 highwaystar.ruAATTgmail.com
- upgrade to version 1.62

* The translation functions will give a warning on any partial codons

* Phylo module now supports the file formats NeXML and CDAO

* New module Bio.UniProt adds parsers for the GAF, GPA and GPI
formats from UniProt-GOA.

* The BioSQL module is now supported in Jython.

* Feature labels on circular GenomeDiagram figures now support
the label_position argument (start, middle or end)

* The code for parsing 3D structures in mmCIF files was updated
to use the Python standard library\'s shlex module instead of C code
using flex.

* The Bio.Sequencing.Applications module now includes a BWA
command line wrapper.

* Bio.motifs supports JASPAR format files with multiple
position-frequence matrices.

Wed Feb 1 13:00:00 2012 saschpeAATTsuse.de
- Ran spec-cleaner
- Set license to MIT (looks like it)

Wed Jan 11 13:00:00 2012 toddrme2178AATTgmail.com
- Cleaned up spec file

Thu Sep 8 14:00:00 2011 alinm.elenaAATTgmail.com
- Initial commit