Bump biopython from 1.83 to 1.84 in /pipeline/seq_retrieval

[dependabot]

Bumps biopython from 1.83 to 1.84.

Changelog

Sourced from biopython's changelog.

28 June 2024: Biopython 1.84

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

Our main documentation, the Biopython Tutorial and Cookbook, has been converted from LaTeX to reStructuredText, and combined with the existing API documentation, into a single more modern and navigable HTML output.

Bio.Blast contains a new parser for BLAST XML output as a replacement for the old parser in Bio.Blast.NCBIXML. The main differences between the parsers is as follows:

• The old parser stores information in a Bio.Blast.NCBIXML.Blast object, with attribute names based on plain-text Blast output. The new parser stores information in a Bio.Blast.Record object. This class follows the DTD that describes the XML in terms of attribute names and dictionary key names, class structure, and object types. This makes it easier to find the detailed description of each field in the NCBI Blast documentation.
• The old parser stores alignment information directly as seen in the BLAST XML output, i.e. as strings with dashes to represent gaps. The new parser stores the alignment information as a Bio.Align.Alignment object, which can then be used to e.g. print the alignment in a different format.

Bio.Blast also contains a new qblast function as a replacement for the old qblast function in Bio.Blast.NCBIWWW. The main difference is that the old qblast function in Bio.Blast.NCBIWWW returns the BLAST search results as Python strings, while the new qblast returns bytes objects. Note that in Python, to parse an XML file it should be opened in binary mode, as the string encoding is specified in the XML data itself. The object returned by the new qblast function can therefore be passed directly to the BLAST parser. Also, this allows data to be downloaded in a binary format such as JSON2, which returns data in a zipped JSON format.

A function called Bio.Phylo.to_igraph has been added to convert a Bio.Phylo.Tree into an igraph.Graph graph, in parallel to the existing function to convert the same object into a networkx graph.

The PDB module's CE Align code for pairwise structure alignment was cleaned up, and the improved CE align code now considers more alignments and selects one of the longer alignments with the smallest RMSD. As a result, users may find alignments with slightly smaller RMSDs when using CE Align.

The PDB module no longer uses the PDB FTP server by default. Instead, the PDB module uses the HTTPS server in most cases. For get_all_assemblies, the PDB module now uses the RCSB PDB Search API <https://search.rcsb.org/#search-api>_ to get all the assemblies.

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[mluypaert]

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