Revisions of python-biopython
- 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.
- 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``.
- 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
- 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
Automatic submission by obs-autosubmit
- Remove ridiculously wide find commands in %prep, which break a lot (binary) files.
computational molecular biology for python
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