forked from pool/python-biopython
177 lines
9.9 KiB
Plaintext
177 lines
9.9 KiB
Plaintext
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Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com
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- Update to version 1.71
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* Encoding issues have been fixed in several parsers when reading data files
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with non-ASCII characters, like accented letters in people's names. This would
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raise ``UnicodeDecodeError: 'ascii' codec can't decode byte ...`` under some
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system locale settings.
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* Bio.KEGG can now parse Gene files.
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* The multiple-sequence-alignment object used by Bio.AlignIO etc now supports
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a per-column annotation dictionary, useful for richly annotated alignments
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in the Stockholm/PFAM format.
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* The SeqRecord object now has a translate method, following the approach used
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for its existing reverse_complement method etc.
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* The output of function ``format_alignment`` in ``Bio.pairwise2`` for displaying
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a pairwise sequence alignment as text now indicates gaps and mis-matches.
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* Bio.SeqIO now supports reading and writing two-line-per-record FASTA files
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under the format name "fasta-2line", useful if you wish to work without
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line-wrapped sequences.
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* Bio.PDB now contains a writer for the mmCIF file format, which has been the
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standard PDB archive format since 2014. This allows structural objects to be
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written out and facilitates conversion between the PDB and mmCIF file formats.
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* Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc
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wrapper and include a new wrapper for fuzzpro.
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* The restriction enzyme list in Bio.Restriction has been updated to the
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November 2017 release of REBASE.
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* New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2)
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were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain
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no dedicated stop codons; the stop codons in these codes have a context
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dependent encoding as either STOP or as amino acid.
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* In this release more of our code is now explicitly available under either our
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original "Biopython License Agreement", or the very similar but more commonly
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used "3-Clause BSD License". See the ``LICENSE.rst`` file for more details.
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* IO functions such as ``SeqIO.parse`` now accept any objects which can be passed
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to the builtin ``open`` function. Specifically, this allows using
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``pathlib.Path`` objects under Python 3.6 and newer, as per `PEP 519
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<https://www.python.org/dev/peps/pep-0519/>`_.
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* Bio.SearchIO can now parse InterProScan XML files.
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* For Python 3 compatibility, comparision operators for the entities within a
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Bio.PDB Structure object were implemented. These allow the comparison of
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models, chains, residues, and atoms with the common operators (==, !=, >, ...)
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Comparisons are based on IDs and take the parents of the entity up to the
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model level into account. For consistent behaviour of all entities the operators
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for atoms were modified to also consider the parent IDs. NOTE: this represents a
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change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic
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the behaviour of previous versions, comparison will have to be done for Atom IDs
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and alternative locations specifically.
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* Additionally, a number of small bugs and typos have been fixed with further
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additions to the test suite, and there has been further work to follow the
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Python PEP8, PEP257 and best practice standard coding style.
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- Update to version 1.70
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* Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our
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original logo and the current Python logo, this shows a yellow and blue snake
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forming a double helix.
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* For installation Biopython now assumes ``setuptools`` is present, and takes
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advantage of this to declare we require NumPy at install time (except under
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Jython). This should help ensure ``pip install biopython`` works smoothly.
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* Bio.AlignIO now supports Mauve's eXtended Multi-FastA (XMFA) file format
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under the format name "mauve" (contributed by Eric Rasche).
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* Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return
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text-mode handles for use under Python 3.
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* Two new arguments for reading and writing blast-xml files have been added
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to the Bio.SearchIO functions (read/parse and write, respectively). They
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are 'use_raw_hit_ids' and 'use_raw_query_ids'. Check out the relevant
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SearchIO.BlastIO documentation for a complete description of what these
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arguments do.
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* Bio.motifs was updated to support changes in MEME v4.11.4 output.
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* The Bio.Seq sequence objects now have a ``.count_overlap()`` method to
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supplement the Python string like non-overlap based ``.count()`` method.
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* The Bio.SeqFeature location objects can now be compared for equality.
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* Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw
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instead, or another library or program if more advanced plotting functionality
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is needed.
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* In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
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_DistanceMatrix) has a new method 'format_phylip' to write Phylip-compatible
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distance matrix files (contributed by Jordan Willis).
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* Additionally, a number of small bugs have been fixed with further additions
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to the test suite, and there has been further work to follow the Python PEP8,
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PEP257 and best practice standard coding style.
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- Use license tag
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-------------------------------------------------------------------
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Wed May 24 14:28:23 UTC 2017 - toddrme2178@gmail.com
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- Implement single-spec version
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- Fix source URL.
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- updated to version 1.69
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* We now expect and take advantage of NumPy under PyPy, and compile most of the
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Biopython C code modules as well.
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* Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the
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format name "maf", using new module Bio.AlignIO.MafIO which also offers
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indexed access to these potentially large files using SQLite3 (contributed by
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Andrew Sczesnak, with additional refinements from Adam Novak).
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* Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The
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underlying format (ABIF) remains the same as AB1 files and so the string
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'abif' is the expected format argument in the main SeqIO functions. AbiIO
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determines whether the file is AB1 or FSA based on the presence of specific
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tags.
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* The Uniprot parser is now able to parse "submittedName" elements in XML files.
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* The NEXUS parser handling of internal node comments has been improved, which
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should help if working with tools like the BEAST TreeAnnotator. Slashes are
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now also allowed in identifiers.
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* New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue,
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and cell line ontology (contributed by Steve Marshall).
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* For consistency the Bio.Seq module now offers a complement function (already
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available as a method on the Seq and MutableSeq objects).
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* The SeqFeature object's qualifiers is now an explicitly ordered dictionary
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(note that as of Python 3.6 the Python dict is ordered by default anyway).
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This helps reproduce GenBank/EMBL files on input/output.
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* The Bio.SeqIO UniProt-XML parser was updated to cope with features with
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unknown locations which can be found in mass spec data.
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* The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type
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from the LOCUS/ID line explicitly in the record.annotations dictionary.
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The Bio.SeqIO EMBL parser was updated to cope with more variants seen in
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patent data files, and the related IMGT parser was updated to cope with
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IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed.
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The GenBank output now uses colon space to match current NCBI DBLINK lines.
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* The Bio.Affy package supports Affymetrix version 4 of the CEL file format,
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in addition to version 3.
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* The restriction enzyme list in Bio.Restriction has been updated to the
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February 2017 release of REBASE.
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* Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default),
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PDBML/XML and mmtf format protein structures. This is inline with the RCSB
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recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython
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already has support for parsing mmCif files.
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* Additionally, a number of small bugs have been fixed with further additions
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to the test suite, and there has been further work to follow the Python PEP8,
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PEP257 and best practice standard coding style.
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-------------------------------------------------------------------
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Thu Nov 17 10:10:59 UTC 2016 - alinm.elena@gmail.com
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- updated to version 1.68
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-------------------------------------------------------------------
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Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com
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- Update to version 1.63
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* 2to3 no longer needed for python 3
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- Added additional dependencies
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-------------------------------------------------------------------
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Thu Sep 19 02:06:32 UTC 2013 - highwaystar.ru@gmail.com
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- upgrade to version 1.62
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* The translation functions will give a warning on any partial codons
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* Phylo module now supports the file formats NeXML and CDAO
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* New module Bio.UniProt adds parsers for the GAF, GPA and GPI
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formats from UniProt-GOA.
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* The BioSQL module is now supported in Jython.
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* Feature labels on circular GenomeDiagram figures now support
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the label_position argument (start, middle or end)
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* The code for parsing 3D structures in mmCIF files was updated
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to use the Python standard library's shlex module instead of C code
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using flex.
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* The Bio.Sequencing.Applications module now includes a BWA
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command line wrapper.
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* Bio.motifs supports JASPAR format files with multiple
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position-frequence matrices.
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-------------------------------------------------------------------
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Wed Feb 1 14:09:33 UTC 2012 - saschpe@suse.de
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- Ran spec-cleaner
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- Set license to MIT (looks like it)
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-------------------------------------------------------------------
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Wed Jan 11 14:56:08 UTC 2012 - toddrme2178@gmail.com
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- Cleaned up spec file
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-------------------------------------------------------------------
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Thu Sep 8 19:36:32 UTC 2011 - alinm.elena@gmail.com
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- Initial commit
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