forked from pool/python-biopython
Matej Cepl
38ef6639e1
(binary) files. OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=11
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-------------------------------------------------------------------
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Tue Nov 3 15:58:16 UTC 2020 - Matej Cepl <mcepl@suse.com>
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- Remove ridiculously wide find commands in %prep, which break a lot
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(binary) files.
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-------------------------------------------------------------------
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Wed Jul 8 07:31:29 UTC 2020 - Marketa Calabkova <mcalabkova@suse.com>
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- Update to version 1.77
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* **We have dropped support for Python 2 now.**
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* ``pairwise2`` now allows the input of parameters with keywords and returns the
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alignments as a list of ``namedtuples``.
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* The codon tables have been updated to NCBI genetic code table version 4.5,
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which adds Cephalodiscidae mitochondrial as table 33.
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* Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
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* A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
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handle protein structure transformations using dihedral angles (internal
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coordinates). The new framework supports lossless interconversion between
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internal and cartesian coordinates, which, among other uses, simplifies the
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analysis and manipulation of coordinates of proteins structures.
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* ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
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output.
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* In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
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now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
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CPUs under Linux thanks to Travis CI. Further post-release testing done by
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Debian and other packagers and distributors of Biopython also covers these
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CPUs.
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* ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
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re-written: it now applies ``.calculate()`` to chunks of the sequence
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to maintain a low memory footprint for long sequences.
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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. There has been further work to follow the Python
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PEP8, PEP257 and best practice standard coding style, and more of the code
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style has been reformatted with the ``black`` tool.
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-------------------------------------------------------------------
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Wed Nov 20 20:17:31 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Update to version 1.75
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* The restriction enzyme list in Bio.Restriction has been updated to the August
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2019 release of REBASE.
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* ``Bio.SeqIO`` now supports reading and writing files in the native format of
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Christian Marck's DNA Strider program ("xdna" format, also used by Serial
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Cloner), as well as reading files in the native formats of GSL Biotech's
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SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").
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* ``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
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format (work funded by the National Marrow Donor Program).
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* The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
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methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
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The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.
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* The ``MMTFIO`` class has been added that allows writing of MMTF file format
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files from a Biopython structure object. ``MMTFIO`` has a similar interface to
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``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
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out a specified selection. This final addition to read/write support for
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PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
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* Values from mmCIF files are now read in as a list even when they consist of a
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single value. This change improves consistency and reduces the likelihood of
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making an error, but will require user code to be updated accordingly.
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* ``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
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PDB-style Astral files.
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* A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
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pretty print method ``format_alignment`` to restore the output of local
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alignments to the 'old' format (showing the whole sequences including the
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un-aligned parts instead of only showing the aligned parts).
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* A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
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``IsoelectricPoint`` in ``Bio.SeqUtils``.
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* The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
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pairwise alignments, i.e. alignments of any Python object, for example
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three-letter amino acid sequences, three-nucleotide codons, and arrays of
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integers.
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* A new module ``substitution_matrices`` was added to ``Bio.Align``, which
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includes an ``Array`` class that can be used as a substitution matrix. As
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the ``Array`` class is a subclass of a numpy array, mathematical operations
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can be applied to it directly, and C code that makes use of substitution
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matrices can directly access the numerical values stored in the substitution
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matrices. This module is intended as a replacement of ``Bio.SubsMat``,
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which is currently unmaintained.
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* As in recent releases, more of our code is now explicitly available under
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either our original "Biopython License Agreement", or the very similar but
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more commonly used "3-Clause BSD License". See the ``LICENSE.rst`` file for
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more details.
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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. We have also
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started to use the ``black`` Python code formatting tool.
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-------------------------------------------------------------------
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Tue Jul 23 01:23:01 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Update to version 1.74
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* Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now
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have a string-like ``.join()`` method.
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* The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning
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the fields may not always follow the historical column based positions. We
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no longer give a warning when parsing these. We now allow writing such files
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(although with a warning as support for reading them is not yet widespread).
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* Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added.
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* We now capture the IDcode field from PDB Header records.
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* ``Bio.pairwise2``'s pretty-print output from ``format_alignment`` has been
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optimized for local alignments: If they do not consist of the whole sequences,
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only the aligned section of the sequences are shown, together with the start
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positions of the sequences (in 1-based notation). Alignments of lists will now
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also be prettily printed.
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* ``Bio.SearchIO`` now supports parsing the text output of the HHsuite protein
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sequence search tool. The format name is ``hhsuite2-text`` and
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``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively.
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* ``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``. This
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attribute is meant for capturing the order by which the HSP were output in the
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parsed file and is set with a default value of -1 for all HSP objects. It is
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also used for sorting the output of ``QueryResult.hsps``.
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* ``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing. The
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goal of this change is make the parser more robust by being able to extract
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string-values that are not utf-8-encoded. This affects all tag values, except
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for ID and description values, where they need to be extracted as strings
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to conform to the ``SeqRecord`` interface. In this case, the parser will
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attempt to decode using ``utf-8`` and fall back to the system encoding if that
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fails. This change affects Python 3 only.
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* ``Bio.motifs.mast`` has been updated to parse XML output files from MAST over
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the plain-text output file. The goal of this change is to parse a more
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structured data source with minimal loss of functionality upon future MAST
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releases. Class structure remains the same plus an additional attribute
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``Record.strand_handling`` required for diagram parsing.
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* ``Bio.Entrez`` now automatically retries HTTP requests on failure. The
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maximum number of tries and the sleep between them can be configured by
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changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.
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(The defaults are 3 tries and 15 seconds, respectively.)
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* All tests using the older print-and-compare approach have been replaced by
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unittests following Python's standard testing framework.
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* On the documentation side, all the public modules, classes, methods and
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functions now have docstrings (built in help strings). Furthermore, the PDF
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version of the *Biopython Tutorial and Cookbook* now uses syntax coloring
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for code snippets.
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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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-------------------------------------------------------------------
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Fri Jan 4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Update to version 1.73
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* As in recent releases, more of our code is now explicitly available under
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either our original "Biopython License Agreement", or the very similar but
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more commonly used "3-Clause BSD License". See the ``LICENSE.rst`` file for
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more details.
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* The dictionary-like indexing in SeqIO and SearchIO will now explicitly preserve
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record order to match a behaviour change in the Python standard dict object.
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This means looping over the index will load the records in the on-disk order,
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which will be much faster (previously it would be effectively at random, based
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on the key hash sorting).
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* The "grant" matrix in Bio.SubsMat.MatrixInfo has been replaced as our original
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values taken from Gerhard Vogt's old webpages at EMBL Heidelberg were
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discovered to be in error. The new values have been transformed following
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Vogt's approach, taking the global maximum 215 minus the similarity scores
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from the original paper Grantham (1974), to give a distance measure.
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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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* Double-quote characters in GenBank feature qualifier values in ``Bio.SeqIO``
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are now escaped as per the NCBI standard. Improperly escaped values trigger a
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warning on parsing.
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* There is a new command line wrapper for the BWA-MEM sequence mapper.
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* The string-based FASTA parsers in ``Bio.SeqIO.FastaIO`` have been optimised,
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which also speeds up parsing FASTA files using ``Bio.SeqIO.parse()``.
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- Update to version 1.72
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* Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
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SeqIO.write (especially when used in a for loop).
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* The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
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inclusive end co-ordinates to better handle searches at end points. This
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will require you to rebuild any existing MAF index files.
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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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* The Entrez module now supports the NCBI API key. Also you can now set a custom
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directory for DTD and XSD files. This allows Entrez to be used in environments
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like AWS Lambda, which restricts write access to specific directories.
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Improved support for parsing NCBI Entrez XML files that use XSD schemas.
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* Internal changes to our C code mean that NumPy is no longer required at
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compile time - only at run time (and only for those modules which use NumPy).
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* Seq, UnknownSeq, MutableSeq and derived classes now support integer
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multiplication methods, matching native Python string methods.
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* A translate method has been added to Bio.SeqFeature that will extract a
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feature and translate it using the codon_start and transl_table qualifiers
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of the feature if they are present.
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* Bio.SearchIO is no longer considered experimental, and so it does not raise
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warnings anymore when imported.
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* A new pairwise sequence aligner is available in Bio.Align, as an alternative
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to the existing pairwise sequence aligner in Bio.pairwise2.
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-------------------------------------------------------------------
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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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