forked from pool/python-biopython
Dirk Mueller
323e9018aa
* 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/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=21
85 lines
2.5 KiB
RPMSpec
85 lines
2.5 KiB
RPMSpec
#
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# spec file for package python-biopython
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#
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# Copyright (c) 2023 SUSE LLC
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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# Tests require a network connection
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%bcond_with test
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%define skip_python2 1
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%define skip_python36 1
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Name: python-biopython
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Version: 1.82
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Release: 0
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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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URL: https://biopython.org/
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Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
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Source100: python-biopython-rpmlintrc
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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module numpy-devel}
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BuildRequires: %{python_module setuptools}
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BuildRequires: %{python_module xml}
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BuildRequires: fdupes
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BuildRequires: flex
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BuildRequires: python-rpm-macros
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Requires: python-numpy
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Requires: python-xml
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Recommends: python-matplotlib
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Recommends: python-mysql
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Recommends: python-networkx
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Recommends: python-psycopg2
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Recommends: python-pydot
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Recommends: python-pygraphviz
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Recommends: python-rdflib
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Recommends: python-reportlab
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%python_subpackages
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%description
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The Biopython Project is an international association of developers of freely
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available Python tools for computational molecular biology.
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%prep
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%setup -q -n biopython-%{version}
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find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
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# Example scripts cannot be in a subdirectory
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mv -v Doc/examples examples
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%build
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export LANG=en_US.UTF-8
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%python_build
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%install
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export LANG=en_US.UTF-8
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%python_install
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%python_expand %fdupes %{buildroot}%{$python_sitearch}
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%if %{with test}
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%check
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export LANG=en_US.UTF-8
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%pytest
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%endif
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%files %{python_files}
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%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
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%doc Doc/ examples/
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%license LICENSE.rst
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%{python_sitearch}/Bio/
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%{python_sitearch}/BioSQL/
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%{python_sitearch}/biopython-%{version}-py*.egg-info
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%changelog
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