python-biopython
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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Filename | Size | Changed |
---|---|---|
biopython-1.82.tar.gz | 0019432124 18.5 MB | |
python-biopython-rpmlintrc | 0000000102 102 Bytes | |
python-biopython.changes | 0000030357 29.6 KB | |
python-biopython.spec | 0000002607 2.55 KB |
Revision 11 (latest revision is 12)
Ana Guerrero (anag+factory)
accepted
request 1135235
from
Dirk Mueller (dirkmueller)
(revision 11)
- 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``.
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