Releases · diegozea/MIToS.jl

MIToS v3.0.0 requires Julia v1.9 or higher, dropping support for older versions. This
release introduces several breaking changes to improve the usability of the package.
When possible, deprecation warnings are used to inform you of the changes.

MIToS.MSA

The MSA module now includes ways to read, write, and work with unaligned protein sequences:

The MSA module now exports the AnnotatedSequence type to represent a single protein
sequence with annotations. This type is a subtype of the new AbstractSequence type,
a subtype of the new AbstractResidueMatrix type.
The MSA module now exports the sequence_id function to get the identifier of a
sequence object.
The MSA module now defines the FASTASequences, PIRSequences, and RawSequences
file formats to read and write (unaligned) protein sequences in FASTA, PIR, and raw
formats, respectively.
[Breaking change] The behavior of the getannotresidue, getannotsequence,
setannotresidue!, and setannotsequence! functions have changed for sequences objects,
such as AnnotatedSequence, AnnotatedAlignedSequence, and AlignedSequence. Now, these
functions take the feature name, rather than the sequence name, as the second
positional argument. As an example of migration,
getannotsequence(sequence, "sequence_name", "feature_name") should be replaced by
getannotsequence(sequence, "feature_name"). You still need to specify the sequence name
when working with MSA objects.

Other changes in the MSA module are:

[Breaking change] The join function for AnnotatedMultipleSequenceAlignment objects
is deprecated in favor of the join_msas function.
[Breaking change] The Clusters type is no longer a subtype of ClusteringResult from
the Clustering.jl package. Instead, the Clusters type is now a subtype of the new
AbstractCluster type. Support for the Clustering.jl interface is still available
through package extensions. You now need to load the Clustering.jl package to use the
assignments, nclusters, and counts functions.

MIToS.PDB

The PDB module now depends on the BioStructures package. The main changes in the PDB
module are:

The PDB module now exports the MMCIFFile file format to read and write PDB files in
the mmCIF format (using BioStructures under the hood).
[Breaking change] The download_alphafold_structure function can now download the
predicted structures from the AlphaFold Protein Structure Database using the mmCIF
format (format=MMCIFFile). This is the new default format. Therefore, you should use
format=PDBFile to get a PDB file like before. For example,
download_alphafold_structure("P00520") in previous versions is the same as
download_alphafold_structure("P00520", format=PDBFile) in this version.
[Breaking change] The downloadpdb function now returns a mmCIF file by default.
Therefore, you should use format=PDBML to get a PDBML file. As an example of migration,
downloadpdb("1IVO") should be replaced by downloadpdb("1IVO", format=PDBML), unless
you want to get a mmCIF file.
[Breaking change] The PDBAtom type now adds two extra fields: alt_id and charge
to represent the alternative location indicator and the atom's charge, respectively.
This improves the compatibility with the mmCIF format and the BioStructures package.
[Breaking change] The query_alphafolddb function now returns the EntrySummary object
of the returned JSON response instead of the Root list. Therefore, there is no need to
take the first element of the list to get the required information. For example,
query_alphafolddb("P00520")[1]["uniprotId"] would be replaced by
query_alphafolddb("P00520")["uniprotId"].

MIToS.Utils.Scripts

[Breaking change] The MIToS.Utils.Scripts module and the MIToS scripts have been
moved to their package at MIToS_Scripts.jl.
Therefore, the MIToS.Utils.Scripts module is no longer exported. This allows for a
reduction in the number of MIToS dependencies, and improved load time.

Assets 2

01 Jul 13:20

github-actions

v2.22.0

b8c96e1

v2.22.0

MIToS v2.22.0

Diff since v2.21.0

This versions introduces several breaking changes to improve the usability of the
Information module. The main changes are:

[Breaking change] The Information module deprecates the Counts type in favor of
the new Frequencies type. The new type as the same signature and behavior as the old one.
[Breaking change] The count function on sequences has been deprecated in favor of the
frequencies function, which has the same signature and behavior as the old one.
[Breaking change] The count! function is deprecated in favor of frequencies!.
The new function use keyword arguments to define the weights and pseudocounts. As an
example of migration, count!(table, weights, pseudocounts, seqs...) should be replaced
by frequencies!(table, seqs..., weights=weights, pseudocounts=pseudocounts).
[Breaking change] The probabilities! method using positional arguments for the
weights, pseudocounts and pseudofrequencies is deprecated in favor the one that uses
keyword arguments. As an example of migration,
probabilities!(table, weights, pseudocounts, pseudofrequencies, seqs...)
should be replaced by
probabilities!(table, seqs..., weights=weights, pseudocounts=pseudocounts, pseudofrequencies=pseudofrequencies).
[Breaking change] The Information has deprecated the entropy method on
Frequencies and Probabilities in favor of the shannon_entropy function. The
definition of the base is now done using the base keyword argument. As an example of
migration, entropy(p, 2) should be replaced by shannon_entropy(p, base=2).
[Breaking change] The marginal_entropy methods based on positional arguments are
deprecated in favor of a method relying on the margin and base keyword arguments.
As an example of migration, marginal_entropy(p, 2, 2.0) should be replaced by
marginal_entropy(p, margin=2, base=2.0).
[Breaking change] The mutual_information method based on positional arguments is
deprecated in favor of a method relying on the base keyword argument. As an example of
migration, mutual_information(p, 2) should be replaced by mutual_information(p, base=2).
[Breaking change] The mapcolpairfreq! and mapseqpairfreq! functions now uses the
boolean usediagonal keyword argument to indicate if the function should be applied to
the diagonal elements of the matrix (the default is true). Before, this was done passing
Val{true} or Val{false} as the last positional argument.
The mapcolfreq!, mapseqfreq!, mapcolpairfreq!, and mapseqpairfreq! methods using
keyword arguments, now pass the extra keyword arguments to the mapped function.
The Information module now exports the mapfreq function that offers a more high-level
interface to the mapcolfreq!, mapseqfreq!, mapcolpairfreq!, and mapseqpairfreq!
functions. This function allows the user to map a function to the residue frequencies or
probabilities of the columns or sequences of an MSA. When rank = 2, the function is
applied to pairs of sequences or columns.
The Information module now exports methods of the shannon_entropy, kullback_leibler,
mutual_information, and normalized_mutual_information functions that take an
AbstractArray{Residue} as input, e.g. an MSA. Those methods use the mapfreq function
under the hood to ease the calculation of the information measures on MSAs.
The frequencies!, frequencies, probabilities!, and probabilities functions now
accept arrays of Residues of any dimension. Therefore, there is no need to use the
vec function to convert the arrays to vectors.
The MSA module now exports the WeightType union type to represent weights.