Revisions of python-biopython
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request 1140102
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Dirk Mueller (dirkmueller)
(revision 24)
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Dirk Mueller (dirkmueller)
committed
(revision 23)
- update to 1.83: * This release reverts the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done without a deprecation period. They are again aliases for .location.strand etc, but trigger deprecation warnings.
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request 1135235
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Dirk Mueller (dirkmueller)
(revision 22)
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Dirk Mueller (dirkmueller)
committed
(revision 21)
- update to 1.82: * The ``inplace`` argument of ``complement`` and ``reverse_complement`` in ``Bio.Seq`` now always default to ``False`` both for ``Seq`` and ``MutableSeq`` objects. To modify a ``MutableSeq`` in-place, use ``inplace=True``. * A new class ``CodonAligner`` was added to ``Bio.Align``. A ``CodonAligner`` object can align a nucleotide sequence to the amino acid sequence it encodes, using a dynamic programming algorithm modeled on ``PairwiseAligner`` to take frame shifts into account. The ``CodonAligner`` returns ``Alignment`` objects. * By calling the new ``mapall`` method on an ``Alignment`` object storing a multiple sequence alignment of amino acid sequences, with nucleotide-to-amino acid alignments generated by ``CodonAligner`` as the argument, a codon-by-codon multiple sequence alignment of nucleotide sequences can be obtained. The new submodule ``Bio.Align.analysis`` provides functions to estimate synonymous and nonsynonymous mutations and to perform the McDonald-Kreitman test on the codon multiple sequence alignments. Together, this provides the same functionality as the ``Bio.codonalign`` module, but uses the standard ``Alignment`` class, and does not rely on regular expression searching to align a nucleotide sequence to an amino acid sequence. * The ``hmmer3-text`` SearchIO format now also extracts the similarity string of the parsed alignments. * HMMER results with the full path to the hmmer executable in the banner are now parsed correctly. * We now have basic type hint annotations in various modules including ``Seq``, ``SeqRecord``, and ``SeqIO``.
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request 1065974
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Dirk Mueller (dirkmueller)
(revision 20)
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Dirk Mueller (dirkmueller)
committed
(revision 19)
- update to 1.81: * The API documentation and the `Biopython Tutorial and Cookbook` have been updated to better annotate use and application of the ``Bio.PDB.internal_coords`` module. * ``Bio.Phylo`` now supports ``Alignment`` and ``MultipleSeqAlignment`` objects as input. * Several improvements and bug fixes to the snapgene parser
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accepted
request 1055870
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Dirk Mueller (dirkmueller)
(revision 18)
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Dirk Mueller (dirkmueller)
committed
(revision 17)
- update to 1.80: * This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has also been tested on PyPy3.7 v7.3.5. * Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align`` to read and write ``Alignment`` objects. * Because dict retains the item order by default since Python3.6, all instances of ``collections.OrderedDict`` have been replaced by either standard ``dict`` or where appropriate by ``collections.defaultsdict``. * The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class`` as a string array since the JASPAR 2018 release. * The Local Composition Complexity functions from ``Bio.SeqUtils`` now uses base 4 log instead of 2 as stated in the original reference Konopka (2005), * Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260 * Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked GZIP files with an internal empty block fixed). * The experimental warning was dropped from ``Bio.phenotype`` (which was new in Biopython 1.67). * Sequences now have a ``defined`` attribute that returns a boolean indicating if the underlying data is defined or not. * The ``Bio.PDB`` module now includes a structural alignment module, using the combinatorial extension algorithm of Shindyalov and Bourne, commonly known as CEAlign. The module allows for two structures to be aligned based solely on their 3D conformation, ie. in a sequence-independent manner. The method is particularly powerful when the structures shared a very low degree of sequence similarity. The new module is available in ``Bio.PDB.CEAligner`` with an interface similar to other 3D superimposition modules. * A new module ``Bio.PDB.qcprot`` implements the QCP superposition algorithm in pure Python, deprecating the existing C implementation. This leads to a slight performance improvement and to much better maintainability. The refactored ``qcprot.QCPSuperimposer`` class has small changes to its API, to better
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request 966669
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Factory Maintainer (factory-maintainer)
(revision 16)
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Dirk Mueller (dirkmueller)
committed
(revision 15)
- update to 1.79: * This is intended to be our final release supporting Python 3.6. It also supports Python 3.7, 3.8 and 3.9, and has also been tested on PyPy3.6.1 v7.1.1. * Detailed list of changes see https://github.com/biopython/biopython/blob/biopython-179/NEWS.rst#1-june-2021-biopython-179
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request 874102
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Matej Cepl (mcepl)
(revision 14)
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Matej Cepl (mcepl)
accepted
request 874100
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andy great (andythe_great)
(revision 13)
- Update to version 1.7.8. * The main change is that Bio.Alphabet is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly. * Bio.SeqIO.parse() is faster with "fastq" format due to small improvements in the Bio.SeqIO.QualityIO module. * The SeqFeature object's .extract() method can now be used for trans-spliced locations via an optional dictionary of references. * As in recent releases, 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. * Additionally, a number of small bugs and typos have been fixed with additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and all of the tests have been reformatted with the black tool to match the main code base. - Skip python36 because numpy no longer support it.
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accepted
request 845786
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Matej Cepl (mcepl)
(revision 12)
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Matej Cepl (mcepl)
committed
(revision 11)
- Remove ridiculously wide find commands in %prep, which break a lot (binary) files.
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request 819448
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Tomáš Chvátal (scarabeus_iv)
(revision 10)
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Tomáš Chvátal (scarabeus_iv)
accepted
request 819377
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Markéta Machová (mcalabkova)
(revision 9)
- Update to version 1.77 * **We have dropped support for Python 2 now.** * ``pairwise2`` now allows the input of parameters with keywords and returns the alignments as a list of ``namedtuples``. * The codon tables have been updated to NCBI genetic code table version 4.5, which adds Cephalodiscidae mitochondrial as table 33. * Updated ``Bio.Restriction`` to the January 2020 release of REBASE. * A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to handle protein structure transformations using dihedral angles (internal coordinates). The new framework supports lossless interconversion between internal and cartesian coordinates, which, among other uses, simplifies the analysis and manipulation of coordinates of proteins structures. * ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/ output. * In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x`` CPUs under Linux thanks to Travis CI. Further post-release testing done by Debian and other packagers and distributors of Biopython also covers these CPUs. * ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been re-written: it now applies ``.calculate()`` to chunks of the sequence to maintain a low memory footprint for long sequences. * Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the ``black`` tool.
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accepted
request 750003
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Todd R (TheBlackCat)
(revision 8)
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Todd R (TheBlackCat)
accepted
request 750002
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Todd R (TheBlackCat)
(revision 7)
Update to version 1.75
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accepted
request 717711
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Todd R (TheBlackCat)
(revision 6)
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Todd R (TheBlackCat)
accepted
request 717710
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Todd R (TheBlackCat)
(revision 5)
- Update to version 1.74 * Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now have a string-like ``.join()`` method. * The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning the fields may not always follow the historical column based positions. We no longer give a warning when parsing these. We now allow writing such files (although with a warning as support for reading them is not yet widespread). * Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added. * We now capture the IDcode field from PDB Header records. * ``Bio.pairwise2``'s pretty-print output from ``format_alignment`` has been optimized for local alignments: If they do not consist of the whole sequences, only the aligned section of the sequences are shown, together with the start positions of the sequences (in 1-based notation). Alignments of lists will now also be prettily printed. * ``Bio.SearchIO`` now supports parsing the text output of the HHsuite protein sequence search tool. The format name is ``hhsuite2-text`` and ``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively. * ``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``. This attribute is meant for capturing the order by which the HSP were output in the parsed file and is set with a default value of -1 for all HSP objects. It is also used for sorting the output of ``QueryResult.hsps``. * ``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing. The goal of this change is make the parser more robust by being able to extract string-values that are not utf-8-encoded. This affects all tag values, except for ID and description values, where they need to be extracted as strings to conform to the ``SeqRecord`` interface. In this case, the parser will attempt to decode using ``utf-8`` and fall back to the system encoding if that fails. This change affects Python 3 only. * ``Bio.motifs.mast`` has been updated to parse XML output files from MAST over the plain-text output file. The goal of this change is to parse a more structured data source with minimal loss of functionality upon future MAST releases. Class structure remains the same plus an additional attribute ``Record.strand_handling`` required for diagram parsing. * ``Bio.Entrez`` now automatically retries HTTP requests on failure. The maximum number of tries and the sleep between them can be configured by changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``. (The defaults are 3 tries and 15 seconds, respectively.) * All tests using the older print-and-compare approach have been replaced by unittests following Python's standard testing framework. * On the documentation side, all the public modules, classes, methods and functions now have docstrings (built in help strings). Furthermore, the PDF version of the *Biopython Tutorial and Cookbook* now uses syntax coloring for code snippets. * 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.
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