177 lines
9.9 KiB
Plaintext
177 lines
9.9 KiB
Plaintext
|
-------------------------------------------------------------------
|
||
|
Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.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
|
||
|
<https://www.python.org/dev/peps/pep-0519/>`_.
|
||
|
* 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 14:28:23 UTC 2017 - toddrme2178@gmail.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 10:10:59 UTC 2016 - alinm.elena@gmail.com
|
||
|
|
||
|
- updated to version 1.68
|
||
|
|
||
|
-------------------------------------------------------------------
|
||
|
Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com
|
||
|
|
||
|
- Update to version 1.63
|
||
|
* 2to3 no longer needed for python 3
|
||
|
- Added additional dependencies
|
||
|
|
||
|
-------------------------------------------------------------------
|
||
|
Thu Sep 19 02:06:32 UTC 2013 - highwaystar.ru@gmail.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 14:09:33 UTC 2012 - saschpe@suse.de
|
||
|
|
||
|
- Ran spec-cleaner
|
||
|
- Set license to MIT (looks like it)
|
||
|
|
||
|
-------------------------------------------------------------------
|
||
|
Wed Jan 11 14:56:08 UTC 2012 - toddrme2178@gmail.com
|
||
|
|
||
|
- Cleaned up spec file
|
||
|
|
||
|
-------------------------------------------------------------------
|
||
|
Thu Sep 8 19:36:32 UTC 2011 - alinm.elena@gmail.com
|
||
|
|
||
|
- Initial commit
|
||
|
|