Accepting request 605802 from devel:languages:python
computational molecular biology for python OBS-URL: https://build.opensuse.org/request/show/605802 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=1
This commit is contained in:
Dominique Leuenberger
Git OBS Bridge
commit
061a2d5331
23
.gitattributes
vendored
Normal file
23
.gitattributes
vendored
Normal file
@ -0,0 +1,23 @@
|
||||
## Default LFS
|
||||
*.7z filter=lfs diff=lfs merge=lfs -text
|
||||
*.bsp filter=lfs diff=lfs merge=lfs -text
|
||||
*.bz2 filter=lfs diff=lfs merge=lfs -text
|
||||
*.gem filter=lfs diff=lfs merge=lfs -text
|
||||
*.gz filter=lfs diff=lfs merge=lfs -text
|
||||
*.jar filter=lfs diff=lfs merge=lfs -text
|
||||
*.lz filter=lfs diff=lfs merge=lfs -text
|
||||
*.lzma filter=lfs diff=lfs merge=lfs -text
|
||||
*.obscpio filter=lfs diff=lfs merge=lfs -text
|
||||
*.oxt filter=lfs diff=lfs merge=lfs -text
|
||||
*.pdf filter=lfs diff=lfs merge=lfs -text
|
||||
*.png filter=lfs diff=lfs merge=lfs -text
|
||||
*.rpm filter=lfs diff=lfs merge=lfs -text
|
||||
*.tbz filter=lfs diff=lfs merge=lfs -text
|
||||
*.tbz2 filter=lfs diff=lfs merge=lfs -text
|
||||
*.tgz filter=lfs diff=lfs merge=lfs -text
|
||||
*.ttf filter=lfs diff=lfs merge=lfs -text
|
||||
*.txz filter=lfs diff=lfs merge=lfs -text
|
||||
*.whl filter=lfs diff=lfs merge=lfs -text
|
||||
*.xz filter=lfs diff=lfs merge=lfs -text
|
||||
*.zip filter=lfs diff=lfs merge=lfs -text
|
||||
*.zst filter=lfs diff=lfs merge=lfs -text
|
||||
1
.gitignore
vendored
Normal file
1
.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
.osc
|
||||
3
biopython-1.71.tar.gz
Normal file
3
biopython-1.71.tar.gz
Normal file
@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033
|
||||
size 16031832
|
||||
176
python-biopython.changes
Normal file
176
python-biopython.changes
Normal file
@ -0,0 +1,176 @@
|
||||
-------------------------------------------------------------------
|
||||
Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com
|
||||
|
||||
- Update to version 1.71
|
||||
* Encoding issues have been fixed in several parsers when reading data files
|
||||
with non-ASCII characters, like accented letters in people's names. This would
|
||||
raise ``UnicodeDecodeError: 'ascii' codec can't decode byte ...`` under some
|
||||
system locale settings.
|
||||
* Bio.KEGG can now parse Gene files.
|
||||
* The multiple-sequence-alignment object used by Bio.AlignIO etc now supports
|
||||
a per-column annotation dictionary, useful for richly annotated alignments
|
||||
in the Stockholm/PFAM format.
|
||||
* The SeqRecord object now has a translate method, following the approach used
|
||||
for its existing reverse_complement method etc.
|
||||
* The output of function ``format_alignment`` in ``Bio.pairwise2`` for displaying
|
||||
a pairwise sequence alignment as text now indicates gaps and mis-matches.
|
||||
* Bio.SeqIO now supports reading and writing two-line-per-record FASTA files
|
||||
under the format name "fasta-2line", useful if you wish to work without
|
||||
line-wrapped sequences.
|
||||
* Bio.PDB now contains a writer for the mmCIF file format, which has been the
|
||||
standard PDB archive format since 2014. This allows structural objects to be
|
||||
written out and facilitates conversion between the PDB and mmCIF file formats.
|
||||
* Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc
|
||||
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)
|
||||
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.
|
||||
* 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.
|
||||
* IO functions such as ``SeqIO.parse`` now accept any objects which can be passed
|
||||
to the builtin ``open`` function. Specifically, this allows using
|
||||
``pathlib.Path`` objects under Python 3.6 and newer, as per `PEP 519
|
||||
<https://www.python.org/dev/peps/pep-0519/>`_.
|
||||
* Bio.SearchIO can now parse InterProScan XML files.
|
||||
* For Python 3 compatibility, comparision operators for the entities within a
|
||||
Bio.PDB Structure object were implemented. These allow the comparison of
|
||||
models, chains, residues, and atoms with the common operators (==, !=, >, ...)
|
||||
Comparisons are based on IDs and take the parents of the entity up to the
|
||||
model level into account. For consistent behaviour of all entities the operators
|
||||
for atoms were modified to also consider the parent IDs. NOTE: this represents a
|
||||
change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic
|
||||
the behaviour of previous versions, comparison will have to be done for Atom IDs
|
||||
and alternative locations specifically.
|
||||
* Additionally, a number of small bugs and typos have been fixed with further
|
||||
additions to the test suite, and there has been further work to follow the
|
||||
Python PEP8, PEP257 and best practice standard coding style.
|
||||
- Update to version 1.70
|
||||
* Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our
|
||||
original logo and the current Python logo, this shows a yellow and blue snake
|
||||
forming a double helix.
|
||||
* For installation Biopython now assumes ``setuptools`` is present, and takes
|
||||
advantage of this to declare we require NumPy at install time (except under
|
||||
Jython). This should help ensure ``pip install biopython`` works smoothly.
|
||||
* Bio.AlignIO now supports Mauve's eXtended Multi-FastA (XMFA) file format
|
||||
under the format name "mauve" (contributed by Eric Rasche).
|
||||
* Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return
|
||||
text-mode handles for use under Python 3.
|
||||
* Two new arguments for reading and writing blast-xml files have been added
|
||||
to the Bio.SearchIO functions (read/parse and write, respectively). They
|
||||
are 'use_raw_hit_ids' and 'use_raw_query_ids'. Check out the relevant
|
||||
SearchIO.BlastIO documentation for a complete description of what these
|
||||
arguments do.
|
||||
* Bio.motifs was updated to support changes in MEME v4.11.4 output.
|
||||
* The Bio.Seq sequence objects now have a ``.count_overlap()`` method to
|
||||
supplement the Python string like non-overlap based ``.count()`` method.
|
||||
* The Bio.SeqFeature location objects can now be compared for equality.
|
||||
* Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw
|
||||
instead, or another library or program if more advanced plotting functionality
|
||||
is needed.
|
||||
* In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
|
||||
_DistanceMatrix) has a new method 'format_phylip' to write Phylip-compatible
|
||||
distance matrix files (contributed by Jordan Willis).
|
||||
* Additionally, a number of small bugs have been fixed with further additions
|
||||
to the test suite, and there has been further work to follow the Python PEP8,
|
||||
PEP257 and best practice standard coding style.
|
||||
- Use license tag
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Wed May 24 14:28:23 UTC 2017 - toddrme2178@gmail.com
|
||||
|
||||
- Implement single-spec version
|
||||
- Fix source URL.
|
||||
- updated to version 1.69
|
||||
* We now expect and take advantage of NumPy under PyPy, and compile most of the
|
||||
Biopython C code modules as well.
|
||||
* Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the
|
||||
format name "maf", using new module Bio.AlignIO.MafIO which also offers
|
||||
indexed access to these potentially large files using SQLite3 (contributed by
|
||||
Andrew Sczesnak, with additional refinements from Adam Novak).
|
||||
* Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The
|
||||
underlying format (ABIF) remains the same as AB1 files and so the string
|
||||
'abif' is the expected format argument in the main SeqIO functions. AbiIO
|
||||
determines whether the file is AB1 or FSA based on the presence of specific
|
||||
tags.
|
||||
* The Uniprot parser is now able to parse "submittedName" elements in XML files.
|
||||
* The NEXUS parser handling of internal node comments has been improved, which
|
||||
should help if working with tools like the BEAST TreeAnnotator. Slashes are
|
||||
now also allowed in identifiers.
|
||||
* New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue,
|
||||
and cell line ontology (contributed by Steve Marshall).
|
||||
* For consistency the Bio.Seq module now offers a complement function (already
|
||||
available as a method on the Seq and MutableSeq objects).
|
||||
* The SeqFeature object's qualifiers is now an explicitly ordered dictionary
|
||||
(note that as of Python 3.6 the Python dict is ordered by default anyway).
|
||||
This helps reproduce GenBank/EMBL files on input/output.
|
||||
* The Bio.SeqIO UniProt-XML parser was updated to cope with features with
|
||||
unknown locations which can be found in mass spec data.
|
||||
* The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type
|
||||
from the LOCUS/ID line explicitly in the record.annotations dictionary.
|
||||
The Bio.SeqIO EMBL parser was updated to cope with more variants seen in
|
||||
patent data files, and the related IMGT parser was updated to cope with
|
||||
IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed.
|
||||
The GenBank output now uses colon space to match current NCBI DBLINK lines.
|
||||
* The Bio.Affy package supports Affymetrix version 4 of the CEL file format,
|
||||
in addition to version 3.
|
||||
* The restriction enzyme list in Bio.Restriction has been updated to the
|
||||
February 2017 release of REBASE.
|
||||
* Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default),
|
||||
PDBML/XML and mmtf format protein structures. This is inline with the RCSB
|
||||
recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython
|
||||
already has support for parsing mmCif files.
|
||||
* Additionally, a number of small bugs have been fixed with further additions
|
||||
to the test suite, and there has been further work to follow the Python PEP8,
|
||||
PEP257 and best practice standard coding style.
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Thu Nov 17 10:10:59 UTC 2016 - alinm.elena@gmail.com
|
||||
|
||||
- updated to version 1.68
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com
|
||||
|
||||
- Update to version 1.63
|
||||
* 2to3 no longer needed for python 3
|
||||
- Added additional dependencies
|
||||
|
||||
-------------------------------------------------------------------
|
||||
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
|
||||
* Phylo module now supports the file formats NeXML and CDAO
|
||||
* 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
|
||||
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
|
||||
using flex.
|
||||
* The Bio.Sequencing.Applications module now includes a BWA
|
||||
command line wrapper.
|
||||
* Bio.motifs supports JASPAR format files with multiple
|
||||
position-frequence matrices.
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Wed Feb 1 14:09:33 UTC 2012 - saschpe@suse.de
|
||||
|
||||
- Ran spec-cleaner
|
||||
- Set license to MIT (looks like it)
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Wed Jan 11 14:56:08 UTC 2012 - toddrme2178@gmail.com
|
||||
|
||||
- Cleaned up spec file
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Thu Sep 8 19:36:32 UTC 2011 - alinm.elena@gmail.com
|
||||
|
||||
- Initial commit
|
||||
|
||||
89
python-biopython.spec
Normal file
89
python-biopython.spec
Normal file
@ -0,0 +1,89 @@
|
||||
#
|
||||
# spec file for package python-biopython
|
||||
#
|
||||
# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
|
||||
#
|
||||
# All modifications and additions to the file contributed by third parties
|
||||
# remain the property of their copyright owners, unless otherwise agreed
|
||||
# upon. The license for this file, and modifications and additions to the
|
||||
# file, is the same license as for the pristine package itself (unless the
|
||||
# license for the pristine package is not an Open Source License, in which
|
||||
# case the license is the MIT License). An "Open Source License" is a
|
||||
# license that conforms to the Open Source Definition (Version 1.9)
|
||||
# published by the Open Source Initiative.
|
||||
|
||||
# Please submit bugfixes or comments via http://bugs.opensuse.org/
|
||||
#
|
||||
|
||||
|
||||
# Tests require a network connection
|
||||
%bcond_with test
|
||||
|
||||
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
|
||||
Name: python-biopython
|
||||
Version: 1.71
|
||||
Release: 0
|
||||
Summary: Python Tools for Computational Molecular Biology
|
||||
License: MIT
|
||||
Group: Development/Libraries/Python
|
||||
Url: http://www.biopython.org
|
||||
Source: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
|
||||
BuildRequires: flex
|
||||
BuildRequires: fdupes
|
||||
BuildRequires: python-rpm-macros
|
||||
BuildRequires: python3-2to3
|
||||
BuildRequires: %{python_module devel}
|
||||
BuildRequires: %{python_module setuptools}
|
||||
BuildRequires: %{python_module numpy-devel}
|
||||
BuildRequires: %{python_module xml}
|
||||
Requires: python-numpy
|
||||
Requires: python-xml
|
||||
Recommends: python-matplotlib
|
||||
Recommends: python-mysql
|
||||
Recommends: python-networkx
|
||||
Recommends: python-psycopg2
|
||||
Recommends: python-pydot
|
||||
Recommends: python-pygraphviz
|
||||
Recommends: python-rdflib
|
||||
Recommends: python-reportlab
|
||||
BuildRoot: %{_tmppath}/%{name}-%{version}-build
|
||||
%python_subpackages
|
||||
|
||||
%description
|
||||
The Biopython Project is an international association of developers of freely
|
||||
available Python tools for computational molecular biology.
|
||||
|
||||
%prep
|
||||
%setup -n biopython-%{version}
|
||||
# remove all execute bits from documentation and fix line endings
|
||||
find -type f -exec chmod -x {} 2>/dev/null ';'
|
||||
find -type f -exec sed -i 's/\r//' {} 2>/dev/null ';'
|
||||
# remove she-bang lines in .py files to keep rpmlint happy
|
||||
find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
|
||||
sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' Scripts/Structure/hsexpo
|
||||
|
||||
%build
|
||||
export LANG=en_US.UTF-8
|
||||
%python_build
|
||||
|
||||
%install
|
||||
export LANG=en_US.UTF-8
|
||||
%python_install
|
||||
%python_expand %fdupes %{buildroot}%{$python_sitelib}
|
||||
|
||||
%if %{with test}
|
||||
%check
|
||||
export LANG=en_US.UTF-8
|
||||
%python_exec setup.py test
|
||||
%endif
|
||||
|
||||
%files %{python_files}
|
||||
%defattr(-,root,root)
|
||||
%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
|
||||
%doc Doc/
|
||||
%license LICENSE.rst
|
||||
%{python_sitearch}/Bio/
|
||||
%{python_sitearch}/BioSQL/
|
||||
%{python_sitearch}/biopython-%{version}-py*.egg-info
|
||||
|
||||
%changelog
|
||||
Loading…
Reference in New Issue
Block a user