Bump biopython from 1.81 to 1.83

[dependabot]

Bumps biopython from 1.81 to 1.83.

Changelog

Sourced from biopython's changelog.

10 January 2024: Biopython 1.83

This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.8 is approaching end of life, our support for it is now deprecated.

This release reverts the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done without a deprecation period. They are again aliases for .location.strand etc, but trigger deprecation warnings.

22 December 2023: Biopython 1.82

This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.8 v7.3.11.

[NOTE: This release unfortunately removed the .strand, .ref, and .ref_db attributes of the SeqFeature without a deprecation period. This has been addressed in Biopython 1.83, which restores them but starts the formal deprecation cycle.]

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. This value is available under the 'similarity' key of the aln_annotation attribute of each HSP, the same as how it is done in other SearchIO formats.

HMMER results with the full path to the hmmer executable in the banner are now parsed correctly. This should help Windows users and users with python installations in non-default locations.

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