Dirk Mueller
323e9018aa
* 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
4 lines
133 B
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4 lines
133 B
Plaintext
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