Numerous bug fixes and enhancements since 3.5
Changes: https://github.com/marcelm/cutadapt/tags
Also replaced ALTERNATIVES with PYTHON_SELF_CONFLICT
ALTERNATIVES does not work automatically and there is no reason
to have more than one installation of py-cutadapt
MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
transcription factor (TF) binding sites. Such sites are generated
by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
(Assay for Transposase Accessible Chromatin Sequencing). MACS
identifies "peaks" in the genome sequence, which are areas enriched
in bound TFs or accessible chromatin.
Minor updates from 2.2.8
Add hacks for cython 3 to pkgsrc patches
This is likely the final release of MACS2
MACS3 package is forthcoming
Changes: https://github.com/macs3-project/MACS/releases
The aim of this project is to implement a versatile high-performance
software library for phylogenetic analysis. The library should serve
as a lower-level interface of PLL (Flouri et al. 2015) and should
have the following properties:
open source code with an appropriate open source license.
64-bit multi-threaded design that handles very large datasets.
easy to use and well-documented.
SIMD implementations of time-consuming parts.
as fast or faster likelihood computations than RAxML (Stamatakis 2014).
fast implementation of the site repeats algorithm (Kobert 2017).
functions for tree visualization.
bindings for Python.
generic and clean design.
Linux, Mac, and Microsoft Windows compatibility.
12 February 2023: Biopython 1.81
===============================================
This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has
also been tested on PyPy3.7 v7.3.5. We intend to drop Python 3.7 support.
The API documentation and the `Biopython Tutorial and Cookbook` have
been updated to better annotate use and application of the
``Bio.PDB.internal_coords`` module.
``Bio.Phylo`` now supports ``Alignment`` and ``MultipleSeqAlignment``
objects as input.
Several improvements and bug fixes to the snapgene parser contributes by
Damien Goutte-Gattat.
Additionally, a number of small bugs and typos have been fixed with additions
to the test suite.
18 November 2022: Biopython 1.80
================================
This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has
also been tested on PyPy3.7 v7.3.5.
Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align`` to
read and write ``Alignment`` objects. String formatting and printing output
of ``Alignment`` objects from ``Bio.Align`` were changed to support these new
functions. To obtain a string showing the aligned sequence with the appropriate
gap characters (as previously shown when calling ``format`` on an alignment),
use ``alignment[i]``, where ``alignment`` is an ``Alignment`` object and ``i``
is the index of the aligned sequence.
Because dict retains the item order by default since Python3.6, all instances
of ``collections.OrderedDict`` have been replaced by either standard ``dict``
or where appropriate by ``collections.defaultsdict``.
Robert Miller has updated the ``Bio.PDB.internal_coords`` module to
make better use of Numpy for lossless structure assembly from dihedral
angles and related internal coordinates. In addition to speeding the
assembly step by ~30%, this adds distance plot support (including
re-generating structures from distance plot data), coordinate space
transforms for superimposing residues and their environments, a
per-chain all-atom array for Atom coordinates, and optional default
values for all internal coordinates. The internal coordinates module
continues to support extracting dihedral angle, bond angle and bond
length (internal coordinates) data, reading/writing structure files of
internal coordinates, and OpenSCAD output of structures for 3D CAD/3D
printing work.
The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class`` as a
string array since the JASPAR 2018 release.
The Local Composition Complexity functions from ``Bio.SeqUtils`` now uses
base 4 log instead of 2 as stated in the original reference Konopka (2005),
Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260
Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked GZIP
files with an internal empty block fixed).
The experimental warning was dropped from ``Bio.phenotype`` (which was new in
Biopython 1.67).
Sequences now have a ``defined`` attribute that returns a boolean indicating
if the underlying data is defined or not.
The ``Bio.PDB`` module now includes a structural alignment module, using the
combinatorial extension algorithm of Shindyalov and Bourne, commonly known as
CEAlign. The module allows for two structures to be aligned based solely on
their 3D conformation, ie. in a sequence-independent manner. The method is
particularly powerful when the structures shared a very low degree of sequence
similarity. The new module is available in ``Bio.PDB.CEAligner`` with an
interface similar to other 3D superimposition modules.
A new module ``Bio.PDB.qcprot`` implements the QCP superposition algorithm in
pure Python, deprecating the existing C implementation. This leads to a slight
performance improvement and to much better maintainability. The refactored
``qcprot.QCPSuperimposer`` class has small changes to its API, to better mirror
that of ``Bio.PDB.Superimposer``.
The ``Bio.PDB.PDBList`` module now allows downloading biological assemblies,
for one or more entries of the wwPDB.
In the ``Bio.Restriction`` module, each restriction enzyme now includes an `id`
property giving the numerical identifier for the REBASE database identifier
from which the enzyme object was created, and a `uri` property with a canonical
`identifiers.org` link to the database, for use in linked-data representations.
Add new ``gc_fraction`` function in ``SeqUtils`` and marks ``GC`` for future
deprecation.
Support for the old format (dating back to 2004) of the GN line in SwissProt
files was dropped in ``Bio.SwissProt``.
Additionally, a number of small bugs and typos have been fixed with additions
to the test suite.
