From 323e9018aa29591d2aec4b669081639658fea17dad96fc3f0edf9d0a0f59c74d Mon Sep 17 00:00:00 2001 From: Dirk Mueller Date: Wed, 27 Dec 2023 09:27:26 +0000 Subject: [PATCH] - 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/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=21 --- biopython-1.81.tar.gz | 3 -- biopython-1.82.tar.gz | 3 ++ python-biopython.changes | 77 ++++++++++++++++++++++++++++++++-------- python-biopython.spec | 2 +- 4 files changed, 66 insertions(+), 19 deletions(-) delete mode 100644 biopython-1.81.tar.gz create mode 100644 biopython-1.82.tar.gz diff --git a/biopython-1.81.tar.gz b/biopython-1.81.tar.gz deleted file mode 100644 index 0280259..0000000 --- a/biopython-1.81.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0 -size 19324875 diff --git a/biopython-1.82.tar.gz b/biopython-1.82.tar.gz new file mode 100644 index 0000000..20bd388 --- /dev/null +++ b/biopython-1.82.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a9b10d959ae88a9744a91c6ce3601f4c86e7ec41679bc93c29f679218f6167bb +size 19432124 diff --git a/python-biopython.changes b/python-biopython.changes index 32703f3..2f16f7f 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,50 @@ +------------------------------------------------------------------- +Wed Dec 27 09:23:42 UTC 2023 - Dirk Müller + +- 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``. + * Calling ``iter`` on a ``PairwiseAlignments`` object returned + by a ``PairwiseAigner`` previously reset the iterator + such that it will start from the first alignment when iterating. + * The MMCIFParser now ignores '.' header values. + * Calling ``set_angle()`` on a residue dihedral angle + previously set only the specified angle, now the default + behavior is to update overlapping angles as well. + * Generating a structure with default internal coordinates, + e.g. from a sequence with ``read_PIC_seq()``, previously + selected wrong default values in many cases. + * Added ``make_extended()`` to set a chain to an extended beta + strand conformation, as the default backbone values reflect + the more popular alpha helix in most cases. + ------------------------------------------------------------------- Wed Feb 15 14:03:39 UTC 2023 - Dirk Müller @@ -63,7 +110,7 @@ Sun Mar 27 13:57:19 UTC 2022 - Dirk Müller - 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 + * Detailed list of changes see https://github.com/biopython/biopython/blob/biopython-179/NEWS.rst#1-june-2021-biopython-179 ------------------------------------------------------------------- @@ -71,13 +118,13 @@ Sat Feb 20 19:29:23 UTC 2021 - andy great - 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 + 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 + * 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 + * 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 + * 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. @@ -304,10 +351,10 @@ Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com wrapper and include a new wrapper for fuzzpro. * The restriction enzyme list in Bio.Restriction has been updated to the November 2017 release of REBASE. - * New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) + * New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain no dedicated stop codons; the stop codons in these codes have a context - dependent encoding as either STOP or as amino acid. + dependent encoding as either STOP or as amino acid. * In this release 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. @@ -410,7 +457,7 @@ Wed May 24 14:28:23 UTC 2017 - toddrme2178@gmail.com ------------------------------------------------------------------- Thu Nov 17 10:10:59 UTC 2016 - alinm.elena@gmail.com -- updated to version 1.68 +- updated to version 1.68 ------------------------------------------------------------------- Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com @@ -423,19 +470,19 @@ Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com Thu Sep 19 02:06:32 UTC 2013 - highwaystar.ru@gmail.com - upgrade to version 1.62 - * The translation functions will give a warning on any partial codons + * The translation functions will give a warning on any partial codons * Phylo module now supports the file formats NeXML and CDAO - * New module Bio.UniProt adds parsers for the GAF, GPA and GPI + * New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats from UniProt-GOA. * The BioSQL module is now supported in Jython. - * Feature labels on circular GenomeDiagram figures now support + * Feature labels on circular GenomeDiagram figures now support the label_position argument (start, middle or end) - * The code for parsing 3D structures in mmCIF files was updated - to use the Python standard library's shlex module instead of C code + * The code for parsing 3D structures in mmCIF files was updated + to use the Python standard library's shlex module instead of C code using flex. - * The Bio.Sequencing.Applications module now includes a BWA + * The Bio.Sequencing.Applications module now includes a BWA command line wrapper. - * Bio.motifs supports JASPAR format files with multiple + * Bio.motifs supports JASPAR format files with multiple position-frequence matrices. ------------------------------------------------------------------- diff --git a/python-biopython.spec b/python-biopython.spec index a1fd36d..56b60d4 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -22,7 +22,7 @@ %define skip_python2 1 %define skip_python36 1 Name: python-biopython -Version: 1.81 +Version: 1.82 Release: 0 Summary: Python Tools for Computational Molecular Biology License: BSD-3-Clause AND MIT