2568d7f53cAccepting request 1206739 from devel:languages:python:numeric
Ana Guerrero
2024-10-10 20:15:08 +0000
34b75af993- update to 1.84: * 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.Dirk Mueller2024-10-10 15:36:57 +0000
893f76b937Accepting request 1140102 from devel:languages:python:numeric
Ana Guerrero
2024-01-21 22:08:49 +0000
07d19599d8- update to 1.83: * 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.Dirk Mueller2024-01-20 12:29:16 +0000
8bcb2d1ddeAccepting request 1135235 from devel:languages:python:numeric
Ana Guerrero
2023-12-28 22:01:16 +0000
323e9018aa- 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`.Dirk Mueller2023-12-27 09:27:26 +0000
39df8ad45aAccepting request 1065974 from devel:languages:python:numeric
Dominique Leuenberger
2023-02-16 15:55:46 +0000
754d74b384- update to 1.81: * The API documentation and the Biopython Tutorial and Cookbook have been updated to better annotate use and application of the `Bio.PDB.internal_coords module. * Bio.Phylo now supports Alignment and MultipleSeqAlignment` objects as input. * Several improvements and bug fixes to the snapgene parserDirk Mueller2023-02-15 14:04:46 +0000
e75d450861Accepting request 1055870 from devel:languages:python:numeric
Dominique Leuenberger
2023-01-04 16:53:47 +0000
e111c6a246- update to 1.80: * This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It has also been tested on PyPy3.7 v7.3.5. * Functions `read, parse, and write were added to Bio.Align to read and write Alignment objects. * Because dict retains the item order by default since Python3.6, all instances of collections.OrderedDict have been replaced by either standard dict or where appropriate by collections.defaultsdict. * The Bio.motifs.jaspar.db now returns tf_family and tf_class as a string array since the JASPAR 2018 release. * The Local Composition Complexity functions from Bio.SeqUtils now uses base 4 log instead of 2 as stated in the original reference Konopka (2005), * Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260 * Append mode is now supported in Bio.bgzf (and a bug parsing blocked GZIP files with an internal empty block fixed). * The experimental warning was dropped from Bio.phenotype (which was new in Biopython 1.67). * Sequences now have a defined attribute that returns a boolean indicating if the underlying data is defined or not. * The Bio.PDB module now includes a structural alignment module, using the combinatorial extension algorithm of Shindyalov and Bourne, commonly known as CEAlign. The module allows for two structures to be aligned based solely on their 3D conformation, ie. in a sequence-independent manner. The method is particularly powerful when the structures shared a very low degree of sequence similarity. The new module is available in Bio.PDB.CEAligner with an interface similar to other 3D superimposition modules. * A new module Bio.PDB.qcprot implements the QCP superposition algorithm in pure Python, deprecating the existing C implementation. This leads to a slight performance improvement and to much better maintainability. The refactored qcprot.QCPSuperimposer` class has small changes to its API, to betterDirk Mueller2023-01-04 14:21:39 +0000
5d32ce3f25Accepting request 966669 from devel:languages:python:numeric
Dominique Leuenberger
2022-04-03 19:31:11 +0000
Ana Guerrero
Dirk Mueller
Dominique Leuenberger
Matej Cepl
Tomáš Chvátal
Todd R