Release 2.24-r1122 (26 December 2021)
-------------------------------------
This release improves alignment around long poorly aligned regions. Older
minimap2 may chain through such regions in rare cases which may result in
missing alignments later. The issue has become worse since the the change of
the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
release provides a better solution with a X-drop-like heuristic and by enabling
two-bandwidth chaining in the assembly mode.
(2.24: 26 December 2021, r1122)
Release 2.23-r1111 (18 November 2021)
-------------------------------------
Notable changes:
* Bugfix: fixed missing alignments around long inversions (#806 and #816).
This bug affected v2.19 through v2.22.
* Improvement: avoid extremely long mapping time for pathologic reads with
highly repeated k-mers not in the reference (#771). Use --q-occ-frac=0
to disable the new heuristic.
* Change: use --cap-kalloc=1g by default.
(2.23: 18 November 2021, r1111)
Release 2.22-r1101 (7 August 2021)
----------------------------------
When choosing the best alignment, this release uses logarithm gap penalty and
query-specific mismatch penalty. It improves the sensitivity to long INDELs in
repetitive regions.
Other notable changes:
* Bugfix: fixed an indirect memory leak that may waste a large amount of
memory given highly repetitive reference such as a 16S RNA database (#749).
All versions of minimap2 have this issue.
* New feature: added --cap-kalloc to reduce the peak memory. This option is
not enabled by default but may become the default in future releases.
Known issue:
* Minimap2 may take a long time to map a read (#771). So far it is not clear
if this happens to v2.18 and earlier versions.
(2.22: 7 August 2021, r1101)
Release 2.21-r1071 (6 July 2021)
--------------------------------
This release fixed a regression in short-read mapping introduced in v2.19
(#776). It also fixed invalid comparisons of uninitialized variables, though
these are harmless (#752). Long-read alignment should be identical to v2.20.
(2.21: 6 July 2021, r1071)
Release 2.20-r1061 (27 May 2021)
--------------------------------
This release fixed a bug in the Python module and improves the command-line
compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset,
users would get alignments more fragmented than v2.18. This could be an issue
for existing pipelines specifying `-r`. This release resolves this issue.
(2.20: 27 May 2021, r1061)
Release 2.19-r1057 (26 May 2021)
--------------------------------
This release includes a few important improvements backported from unimap:
* Improvement: more contiguous alignment through long INDELs. This is enabled
by the minigraph chaining algorithm. All `asm*` presets now use the new
algorithm. They can find INDELs up to 100kb and may be faster for
chromosome-long contigs. The default mode and `map*` presets use this
algorithm to replace the long-join heuristic.
* Improvement: better alignment in highly repetitive regions by rescuing
high-occurrence seeds. If the distance between two adjacent seeds is too
large, attempt to choose a fraction of high-occurrence seeds in-between.
Minimap2 now produces fewer clippings and alignment break points in long
satellite regions.
* Improvement: allow to specify an interval of k-mer occurrences with `-U`.
For repeat-rich genomes, the automatic k-mer occurrence threshold determined
by `-f` may be too large and makes alignment impractically slow. The new
option protects against such cases. Enabled for `asm*` and `map-hifi`.
* New feature: added the `map-hifi` preset for maping PacBio High-Fidelity
(HiFi) reads.
* Change to the default: apply `--cap-sw-mem=100m` for genomic alignment.
* Bugfix: minimap2 could not generate an index file with `-xsr` (#734).
This release represents the most signficant algorithmic change since v2.1 in
2017. With features backported from unimap, minimap2 now has similar power to
unimap for contig alignment. Unimap will remain an experimental project and is
no longer recommended over minimap2. Sorry for reverting the recommendation in
short time.
(2.19: 26 May 2021, r1057)
1 June 2021: Biopython 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.
The ``Seq`` and ``MutableSeq`` classes in ``Bio.Seq`` now store their sequence
contents as ``bytes` ` and ``bytearray`` objects, respectively. Previously, for
``Seq`` objects a string object was used, and a Unicode array object for
``MutableSeq`` objects. This was maintained during the transition from Python2
to Python3. However, a Python2 string object corresponds to a ``bytes`` object
in Python3, storing the string as a series of 256-bit characters. While non-
ASCII characters could be stored in Python2 strings, they were not treated as
such. For example:
In Python2::
>>> s = "Генетика"
>>> type(s)
<class 'str'>
>>> len(s)
16
In Python3::
>>> s = "Генетика"
>>> type(s)
<class 'str'>
>>> len(s)
8
In Python3, storing the sequence contents as ``bytes`` and ``bytearray``
objects has the further advantage that both support the buffer protocol.
Taking advantage of the similarity between ``bytes`` and ``bytearray``, the
``Seq`` and ``MutableSeq`` classes now inherit from an abstract base class
``_SeqAbstractBaseClass`` in ``Bio.Seq`` that implements most of the ``Seq``
and ``MutableSeq`` methods, ensuring their consistency with each other. For
methods that modify the sequence contents, an optional ``inplace`` argument to
specify if a new sequence object should be returned with the new sequence
contents (if ``inplace`` is ``False``, the default) or if the sequence object
itself should be modified (if ``inplace`` is ``True``). For ``Seq`` objects,
which are immutable, using ``inplace=True`` raises an exception. For
``inplace=False``, the default, ``Seq`` objects and ``MutableSeq`` behave
consistently.
As before, ``Seq`` and ``MutableSeq`` objects can be initialized using a string
object, which will be converted to a ``bytes`` or ``bytearray`` object assuming
an ASCII encoding. Alternatively, a ``bytes`` or ``bytearray`` object can be
used, or an instance of any class inheriting from the new
``SequenceDataAbstractBaseClass`` abstract base class in ``Bio.Seq``. This
requires that the class implements the ``__len__`` and ``__getitem`` methods
that return the sequence length and sequence contents on demand. Initialzing a
``Seq`` instance using an instance of a class inheriting from
``SequenceDataAbstractBaseClass`` allows the ``Seq`` object to be lazy, meaning
that its sequence is provided on demand only, without requiring to initialize
the full sequence. This feature is now used in ``BioSQL``, providing on-demand
sequence loading from an SQL database, as well as in a new parser for twoBit
(.2bit) sequence data added to ``Bio.SeqIO``. This is a lazy parser that allows
fast access to genome-size DNA sequence files by not having to read the full
genome sequence. The new ``_UndefinedSequenceData`` class in ``Bio.Seq`` also
inherits from ``SequenceDataAbstractBaseClass`` to represent sequences of known
length but unknown sequence contents. This provides an alternative to
``UnknownSeq``, which is now deprecated as its definition was ambiguous. For
example, in these examples the ``UnknownSeq`` is interpreted as a sequence with
a well-defined sequence contents::
>>> s = UnknownSeq(3, character="A")
>>> s.translate()
UnknownSeq(1, character='K')
>>> s + "A"
Seq("AAAA")
A sequence object with an undefined sequence contents can now be created by
using ``None`` when creating the ``Seq`` object, together with the sequence
length. Trying to access its sequence contents raises an
``UndefinedSequenceError``::
>>> s = Seq(None, length=6)
>>> s
Seq(None, length=6)
>>> len(s)
6
>>> "A" in s
Traceback (most recent call last):
...
Bio.Seq.UndefinedSequenceError: Sequence content is undefined
>>> print(s)
Traceback (most recent call last):
....
Bio.Seq.UndefinedSequenceError: Sequence content is undefined
Element assignment in Bio.PDB.Atom now returns "X" when the element cannot be
unambiguously guessed from the atom name, in accordance with PDB structures.
Bio.PDB entities now have a ``center_of_mass()`` method that calculates either
centers of gravity or geometry.
New method ``disordered_remove()`` implemented in Bio.PDB DisorderedAtom and
DisorderedResidue to remove children.
New module Bio.PDB.SASA implements the Shrake-Rupley algorithm to calculate
atomic solvent accessible areas without third-party tools.
Expected ``TypeError`` behaviour has been restored to the ``Seq`` object's
string like methods (fixing a regression in Biopython 1.78).
The KEGG ``KGML_Pathway`` KGML output was fixed to produce output that complies
with KGML v0.7.2.
Parsing motifs in ``pfm-four-rows`` format can now handle motifs with values
in scientific notation.
Parsing motifs in ``minimal``` MEME format will use ``nsites`` when making
the count matrix from the frequency matrix, instead of multiply the frequency
matrix by 1000000.
Bio.UniProt.GOA now parses Gene Product Information (GPI) files version 1.2,
files can be downloaded from the EBI ftp site:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
4 September 2020: Biopython 1.78
================================
This release of Biopython supports Python 3.6, 3.7 and 3.8. It has also been
tested on PyPy3.6.1 v7.1.1.
The main change is that ``Bio.Alphabet`` is no longer used. In some cases you
will now have to specify expected letters, molecule type (DNA, RNA, protein),
or gap character explicitly. Please consult the updated Tutorial and API
documentation for guidance. This simplification has sped up many ``Seq``
object methods. See https://biopython.org/wiki/Alphabet for more information.
``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
trans-spliced locations via an optional dictionary of references.
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.
Additionally, a number of small bugs and typos have been fixed with additions
to the test suite. There has been further work to follow the Python PEP8,
PEP257 and best practice standard coding style, and all of the tests have
been reformatted with the ``black`` tool to match the main code base.
25 May 2020: Biopython 1.77
===========================
This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been
tested on PyPy3.6.1 v7.1.1-beta0.
**We have dropped support for Python 2 now.**
``pairwise2`` now allows the input of parameters with keywords and returns the
alignments as a list of ``namedtuples``.
The codon tables have been updated to NCBI genetic code table version 4.5,
which adds Cephalodiscidae mitochondrial as table 33.
Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
handle protein structure transformations using dihedral angles (internal
coordinates). The new framework supports lossless interconversion between
internal and cartesian coordinates, which, among other uses, simplifies the
analysis and manipulation of coordinates of proteins structures.
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.
Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and all the main code
base has been reformatted with the ``black`` tool.
20 December 2019: Biopython 1.76
================================
This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has
also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.
We intend this to be our final release supporting Python 2.7 and 3.5.
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.
``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
output.
In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
CPUs under Linux thanks to Travis CI. Further post-release testing done by
Debian and other packagers and distributors of Biopython also covers these
CPUs.
``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
re-written: it now applies ``.calculate()`` to chunks of the sequence
to maintain a low memory footprint for long sequences.
Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and more of the code
style has been reformatted with the ``black`` tool.
6 November 2019: Biopython 1.75
===============================
This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected
to work on the soon to be released Python 3.8. It has also been tested on
PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.
Note we intend to drop Python 2.7 support in early 2020.
The restriction enzyme list in ``Bio.Restriction`` has been updated to the
August 2019 release of REBASE.
``Bio.SeqIO`` now supports reading and writing files in the native format of
Christian Marck's DNA Strider program ("xdna" format, also used by Serial
Cloner), as well as reading files in the native formats of GSL Biotech's
SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").
``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
format (work funded by the National Marrow Donor Program).
The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.
The ``MMTFIO`` class has been added that allows writing of MMTF file format
files from a Biopython structure object. ``MMTFIO`` has a similar interface to
``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
out a specified selection. This final addition to read/write support for
PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
Values from mmCIF files are now read in as a list even when they consist of a
single value. This change improves consistency and reduces the likelihood of
making an error, but will require user code to be updated accordingly.
`Bio.motifs.meme` has been updated to parse XML output files from MEME over
the plain-text output file. The goal of this change is to parse a more
structured data source with minimal loss of functionality upon future MEME
releases.
``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
PDB-style Astral files.
A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
pretty print method ``format_alignment`` to restore the output of local
alignments to the 'old' format (showing the whole sequences including the
un-aligned parts instead of only showing the aligned parts).
A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
``IsoelectricPoint`` in ``Bio.SeqUtils``.
The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
pairwise alignments, i.e. alignments of any Python object, for example
three-letter amino acid sequences, three-nucleotide codons, and arrays of
integers.
A new module ``substitution_matrices`` was added to ``Bio.Align``, which
includes an ``Array`` class that can be used as a substitution matrix. As
the ``Array`` class is a subclass of a numpy array, mathematical operations
can be applied to it directly, and C code that makes use of substitution
matrices can directly access the numerical values stored in the substitution
matrices. This module is intended as a replacement of ``Bio.SubsMat``,
which is currently unmaintained.
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.
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. We have also
started to use the ``black`` Python code formatting tool.
This package is from 2012, the current version is from 2020.
A replacement candidate is in wip/py-mol but needs more work.
One of the last users of py-numpy16 in pkgsrc.
v3.5 (2021-09-29)
-----------------
* :issue:`555`: Add support for dumping statistics in JSON format using ``--json``.
* :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also
add statistics for reads discarded because of ``--discard-untrimmed`` and
``--discard-trimmed``. With this, the numbers in that section should add up to 100%.
* Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 that is
different from the one for R1.
* :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write
``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only.
* :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain
more than one adapter.
* :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores.
* :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.
This flag should be set for packages that import pkg_resources
and thus need setuptools after the build step.
Set this flag for packages that need it and bump PKGREVISION.
Updates for evolving libxtend and biolibc APIs
Add --version flag
Filter out unused SAM fields on input
Numerous other minor fixes and enhancements
Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4
Version 2.2.0
Changes
-------
* Data elements with a VR of **AT** must now be set with values
acceptable to :func:`~pydicom.tag.Tag`, and are always stored as a
:class:`~pydicom.tag.BaseTag`. Previously, any Python type could be
set.
* :meth:`BaseTag.__eq__()<pydicom.tag.BaseTag.__eq__>` returns ``False`` rather
than raising an exception when the operand cannot be converted to
:class:`~pydicom.tag.BaseTag` (:pr:`1327`)
* :meth:`DA.__str__()<pydicom.valuerep.DA.__str__>`,
:meth:`DT.__str__()<pydicom.valuerep.DT.__str__>` and
:meth:`TM.__str__()<pydicom.valuerep.TM.__str__>` return valid DICOM
strings instead of the formatted date and time representations
(:issue:`1262`)
* If comparing :class:`~pydicom.dataset.FileDataset` instances, the file
metadata is now ignored. This makes it possible to compare a
:class:`~pydicom.dataset.FileDataset` object with a
:class:`~pydicom.dataset.Dataset` object.
* :func:`~pydicom.pixel_data_handlers.rle_handler.rle_encode_frame` is
deprecated and will be removed in v3.0, use
:meth:`~pydicom.dataset.Dataset.compress` or
:attr:`~pydicom.encoders.RLELosslessEncoder` instead.
* :func:`~pydicom.filereader.read_file` is deprecated and will be removed in
v3.0, use :func:`~pydicom.filereader.dcmread` instead.
* :func:`~pydicom.filewriter.write_file` is deprecated and will be removed in
v3.0, use :func:`~pydicom.filewriter.dcmwrite` instead.
* Data dictionaries updated to version 2021b of the DICOM Standard
* :class:`~pydicom.dataset.Dataset` no longer inherits from :class:`dict`
Enhancements
------------
* Added a command-line interface for pydicom. Current subcommands are:
* ``show``: display all or part of a DICOM file
* ``codify`` to produce Python code for writing files or sequence items
from scratch.
Please see the :ref:`cli_guide` for examples and details
of all the options for each command.
* A field containing an invalid number of bytes will result in a warning
instead of an exception when
:attr:`~pydicom.config.convert_wrong_length_to_UN` is set to ``True``.
* Private tags known via the private dictionary will now get the configured
VR if read from a dataset instead of **UN** (:issue:`1051`).
* While reading explicit VR, a switch to implicit VR will be silently attempted
if the VR bytes are not valid VR characters, and config option
:attr:`~pydicom.config.assume_implicit_vr_switch` is ``True`` (default)
* New functionality to help with correct formatting of decimal strings (**DS**)
* Added :func:`~pydicom.valuerep.is_valid_ds` to check whether a string is
valid as a DICOM decimal string and
:func:`~pydicom.valuerep.format_number_as_ds` to format a given ``float``
or ``Decimal`` as a DS while retaining the highest possible level of
precision
* If :attr:`~pydicom.config.enforce_valid_values` is set to ``True``, all
**DS** objects created will be checked for the validity of their string
representations.
* Added optional ``auto_format`` parameter to the init methods of
:class:`~pydicom.valuerep.DSfloat` and
:class:`~pydicom.valuerep.DSdecimal` and the :func:`~pydicom.valuerep.DS`
factory function to allow explicitly requesting automatic formatting of
the string representations of these objects when they are constructed.
* Added methods to construct :class:`~pydicom.valuerep.PersonName` objects
from individual components of names (``family_name``, ``given_name``, etc.).
See :meth:`~pydicom.valuerep.PersonName.from_named_components` and
:meth:`~pydicom.valuerep.PersonName.from_named_components_veterinary`.
* Added support for downloading the large test files with the `requests
<https://docs.python-requests.org/en/master/>`_ package in addition to
:mod:`urllib.request` (:pr:`1340`)
* Ensured :func:`~pydicom.pixel_data_handlers.util.convert_color_space` uses
32-bit floats for calculation, added `per_frame` flag to allow frame-by-frame
processing and improved the speed by ~20-60% (:issue:`1348`)
* Optimisations for RLE encoding using *pydicom* (~40% faster).
* Added support for faster decoding (~4-5x) and encoding (~20x) of *RLE Lossless*
*Pixel Data* via the `pylibjpeg-rle
<https://github.com/pydicom/pylibjpeg-rle>`_ plugin (:pr:`1361`, :pr:`1372`).
* Added :func:`Dataset.compress()<pydicom.dataset.Dataset.compress>` function for
compressing uncompressed pixel data using a given encoding format as specified
by a UID. Only *RLE Lossless* is currently supported (:pr:`1372`)
* Added :mod:`~pydicom.encoders` module and the following encoders:
* :attr:`~pydicom.encoders.RLELosslessEncoder` with 'pydicom', 'pylibjpeg'
and 'gdcm' plugins
* Added `read` parameter to :func:`~pydicom.data.get_testdata_file`
to allow reading and returning the corresponding dataset (:pr:`1372`)
* Handle decoded RLE segments with padding (:issue:`1438`)
* Add option to JSON functions to suppress exception and continue (:pr:`1332`)
* Allow searching :class:`~pydicom.fileset.FileSet` s for a list of elements (:pr:`1428`)
* Added hash function to SR :class:`~pydicom.sr.Code` (:pr:`1434`)
Fixes
-----
* Fixed pickling a :class:`~pydicom.dataset.Dataset` instance with sequences
after the sequence had been read (:issue:`1278`)
* Fixed JSON export of numeric values
* Fixed handling of sequences of unknown length that switch to implicit
encoding, and sequences with VR **UN** (:issue:`1312`)
* Do not load external data sources until needed - fixes problems with
standard workflow if `setuptools` are not installed (:issue:`1341`)
* Fixed empty **PN** elements read from file being :class:`str` rather than
:class:`~pydicom.valuerep.PersonName` (:issue:`1338`)
* Fixed handling of JPEG (10918-1) images compressed using RGB colourspace
rather than YBR with the Pillow pixel data handler (:pr:`878`)
* Allow to deepcopy a `~pydicom.dataset.FileDataset` object (:issue:`1147`)
* Fixed elements with a VR of **OL**, **OD** and **OV** not being set correctly
when an encoded backslash was part of the element value (:issue:`1412`)
* Fixed expansion of linear segments with floating point steps in
segmented LUTs (:issue:`1415`)
* Fixed handling of code extensions with person name component delimiter
(:pr:`1449`)
* Fixed bug decoding RBG jpg with APP14 marker due to change in Pillow (:pr:`1444`)
* Fixed decoding for `FloatPixelData` and `DoubleFloatPixelData` via
`pydicom.pixel_data_handlers.numpy_handler` (:issue:`1457`)
Biolibc-tools is a collection of simple, fast, and memory-efficient
programs for processing biological data. These programs built on
biolibc are not complex enough to warrant separate projects.
