Accepting request 1135235 from devel:languages:python:numeric
- 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``. OBS-URL: https://build.opensuse.org/request/show/1135235 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=11
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-------------------------------------------------------------------
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Wed Dec 27 09:23:42 UTC 2023 - Dirk Müller <dmueller@suse.com>
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- update to 1.82:
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* The ``inplace`` argument of ``complement`` and
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``reverse_complement`` in ``Bio.Seq`` now always default to
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``False`` both for ``Seq`` and ``MutableSeq`` objects.
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To modify a ``MutableSeq`` in-place, use ``inplace=True``.
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* A new class ``CodonAligner`` was added to ``Bio.Align``. A
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``CodonAligner`` object can align a nucleotide sequence to the
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amino acid sequence it encodes, using a dynamic programming
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algorithm modeled on ``PairwiseAligner`` to take frame shifts
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into account. The ``CodonAligner`` returns ``Alignment``
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objects.
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* By calling the new ``mapall`` method on an ``Alignment``
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object storing a multiple sequence alignment of amino acid
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sequences, with nucleotide-to-amino acid alignments generated
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by ``CodonAligner`` as the argument, a codon-by-codon
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multiple sequence alignment of nucleotide sequences can be
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obtained. The new submodule ``Bio.Align.analysis`` provides
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functions to estimate synonymous and nonsynonymous mutations
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and to perform the McDonald-Kreitman test on the codon
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multiple sequence alignments. Together, this provides the
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same functionality as the ``Bio.codonalign`` module, but uses
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the standard ``Alignment`` class, and does not rely on regular
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expression searching to align a nucleotide sequence to
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an amino acid sequence.
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* The ``hmmer3-text`` SearchIO format now also extracts the
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similarity string of the parsed alignments.
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* HMMER results with the full path to the hmmer executable in
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the banner are now parsed correctly.
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* We now have basic type hint annotations in various modules
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including ``Seq``, ``SeqRecord``, and ``SeqIO``.
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* Calling ``iter`` on a ``PairwiseAlignments`` object returned
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by a ``PairwiseAigner`` previously reset the iterator
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such that it will start from the first alignment when iterating.
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* The MMCIFParser now ignores '.' header values.
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* Calling ``set_angle()`` on a residue dihedral angle
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previously set only the specified angle, now the default
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behavior is to update overlapping angles as well.
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* Generating a structure with default internal coordinates,
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e.g. from a sequence with ``read_PIC_seq()``, previously
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selected wrong default values in many cases.
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* Added ``make_extended()`` to set a chain to an extended beta
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strand conformation, as the default backbone values reflect
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the more popular alpha helix in most cases.
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-------------------------------------------------------------------
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-------------------------------------------------------------------
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Wed Feb 15 14:03:39 UTC 2023 - Dirk Müller <dmueller@suse.com>
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Wed Feb 15 14:03:39 UTC 2023 - Dirk Müller <dmueller@suse.com>
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@ -22,7 +22,7 @@
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%define skip_python2 1
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%define skip_python2 1
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%define skip_python36 1
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%define skip_python36 1
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Name: python-biopython
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Name: python-biopython
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Version: 1.81
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Version: 1.82
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Release: 0
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Release: 0
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Summary: Python Tools for Computational Molecular Biology
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Summary: Python Tools for Computational Molecular Biology
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License: BSD-3-Clause AND MIT
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License: BSD-3-Clause AND MIT
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