pool/python-biopython
SHA256
2
0
Fork 1
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

- update to 1.82:

Browse Source 
* 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
This commit is contained in:
Dirk Mueller 2023-12-27 09:27:26 +00:00 committed by Git OBS Bridge
parent 754d74b384
commit 323e9018aa
4 changed files with 66 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
biopython-1.81.tar.gz
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0
size 19324875

3
biopython-1.82.tar.gz Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:a9b10d959ae88a9744a91c6ce3601f4c86e7ec41679bc93c29f679218f6167bb
size 19432124

77
python-biopython.changes
View File

@ -1,3 +1,50 @@
-------------------------------------------------------------------
Wed Dec 27 09:23:42 UTC 2023 - Dirk Müller <dmueller@suse.com>
- 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 <dmueller@suse.com>
@ -63,7 +110,7 @@ Sun Mar 27 13:57:19 UTC 2022 - Dirk Müller <dmueller@suse.com>
- 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 <andythe_great@pm.me>
- 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.
-------------------------------------------------------------------

2
python-biopython.spec
View File

@ -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