Changelog for python2-biopython-1.71-3.3.i586.rpm :

* Wed May 09 2018 toddrme2178AATTgmail.com- Update to version 1.71
* Encoding issues have been fixed in several parsers when reading data files with non-ASCII characters, like accented letters in people\'s names. This would raise ``UnicodeDecodeError: \'ascii\' codec can\'t decode byte ...`` under some system locale settings.
* Bio.KEGG can now parse Gene files.
* The multiple-sequence-alignment object used by Bio.AlignIO etc now supports a per-column annotation dictionary, useful for richly annotated alignments in the Stockholm/PFAM format.
* The SeqRecord object now has a translate method, following the approach used for its existing reverse_complement method etc.
* The output of function ``format_alignment`` in ``Bio.pairwise2`` for displaying a pairwise sequence alignment as text now indicates gaps and mis-matches.
* Bio.SeqIO now supports reading and writing two-line-per-record FASTA files under the format name \"fasta-2line\", useful if you wish to work without line-wrapped sequences.
* Bio.PDB now contains a writer for the mmCIF file format, which has been the standard PDB archive format since 2014. This allows structural objects to be written out and facilitates conversion between the PDB and mmCIF file formats.
* Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc wrapper and include a new wrapper for fuzzpro.
* The restriction enzyme list in Bio.Restriction has been updated to the November 2017 release of REBASE.
* New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain no dedicated stop codons; the stop codons in these codes have a context dependent encoding as either STOP or as amino acid.
* 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.
* IO functions such as ``SeqIO.parse`` now accept any objects which can be passed to the builtin ``open`` function. Specifically, this allows using ``pathlib.Path`` objects under Python 3.6 and newer, as per `PEP 519 `_.
* Bio.SearchIO can now parse InterProScan XML files.
* For Python 3 compatibility, comparision operators for the entities within a Bio.PDB Structure object were implemented. These allow the comparison of models, chains, residues, and atoms with the common operators (==, !=, >, ...) Comparisons are based on IDs and take the parents of the entity up to the model level into account. For consistent behaviour of all entities the operators for atoms were modified to also consider the parent IDs. NOTE: this represents a change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic the behaviour of previous versions, comparison will have to be done for Atom IDs and alternative locations specifically.
* Additionally, a number of small bugs and typos 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.- Update to version 1.70
* Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our original logo and the current Python logo, this shows a yellow and blue snake forming a double helix.
* For installation Biopython now assumes ``setuptools`` is present, and takes advantage of this to declare we require NumPy at install time (except under Jython). This should help ensure ``pip install biopython`` works smoothly.
* Bio.AlignIO now supports Mauve\'s eXtended Multi-FastA (XMFA) file format under the format name \"mauve\" (contributed by Eric Rasche).
* Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return text-mode handles for use under Python 3.
* Two new arguments for reading and writing blast-xml files have been added to the Bio.SearchIO functions (read/parse and write, respectively). They are \'use_raw_hit_ids\' and \'use_raw_query_ids\'. Check out the relevant SearchIO.BlastIO documentation for a complete description of what these arguments do.
* Bio.motifs was updated to support changes in MEME v4.11.4 output.
* The Bio.Seq sequence objects now have a ``.count_overlap()`` method to supplement the Python string like non-overlap based ``.count()`` method.
* The Bio.SeqFeature location objects can now be compared for equality.
* Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw instead, or another library or program if more advanced plotting functionality is needed.
* In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously _DistanceMatrix) has a new method \'format_phylip\' to write Phylip-compatible distance matrix files (contributed by Jordan Willis).
* 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.- Use license tag
* Wed May 24 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 2016 alinm.elenaAATTgmail.com- updated to version 1.68
* Mon Dec 09 2013 toddrme2178AATTgmail.com- Update to version 1.63
* 2to3 no longer needed for python 3- Added additional dependencies
* Thu Sep 19 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 01 2012 saschpeAATTsuse.de- Ran spec-cleaner- Set license to MIT (looks like it)
* Wed Jan 11 2012 toddrme2178AATTgmail.com- Cleaned up spec file
* Thu Sep 08 2011 alinm.elenaAATTgmail.com- Initial commit