Recent Releases of MIToS
MIToS - v3.0.0
MIToS v3.0.0
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
MSAmodule now exports theAnnotatedSequencetype to represent a single protein sequence with annotations. This type is a subtype of the newAbstractSequencetype, a subtype of the newAbstractResidueMatrixtype.The
MSAmodule now exports thesequence_idfunction to get the identifier of a sequence object.The
MSAmodule now defines theFASTASequences,PIRSequences, andRawSequencesfile formats to read and write (unaligned) protein sequences in FASTA, PIR, and raw formats, respectively.[Breaking change] The behavior of the
getannotresidue,getannotsequence,setannotresidue!, andsetannotsequence!functions have changed for sequences objects, such asAnnotatedSequence,AnnotatedAlignedSequence, andAlignedSequence. 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 bygetannotsequence(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
joinfunction forAnnotatedMultipleSequenceAlignmentobjects is deprecated in favor of thejoin_msasfunction.[Breaking change] The
Clusterstype is no longer a subtype ofClusteringResultfrom theClustering.jlpackage. Instead, theClusterstype is now a subtype of the newAbstractClustertype. Support for theClustering.jlinterface is still available through package extensions. You now need to load theClustering.jlpackage to use theassignments,nclusters, andcountsfunctions.
MIToS.PDB
The PDB module now depends on the BioStructures package. The main changes in the PDB
module are:
The
PDBmodule now exports theMMCIFFilefile format to read and write PDB files in the mmCIF format (usingBioStructuresunder the hood).[Breaking change] The
download_alphafold_structurefunction 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 useformat=PDBFileto get a PDB file like before. For example,download_alphafold_structure("P00520")in previous versions is the same asdownload_alphafold_structure("P00520", format=PDBFile)in this version.[Breaking change] The
downloadpdbfunction now returns a mmCIF file by default. Therefore, you should useformat=PDBMLto get a PDBML file. As an example of migration,downloadpdb("1IVO")should be replaced bydownloadpdb("1IVO", format=PDBML), unless you want to get a mmCIF file.[Breaking change] The
PDBAtomtype now adds two extra fields:alt_idandchargeto represent the alternative location indicator and the atom's charge, respectively. This improves the compatibility with the mmCIF format and theBioStructurespackage.[Breaking change] The
query_alphafolddbfunction 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 byquery_alphafolddb("P00520")["uniprotId"].
MIToS.Utils.Scripts
- [Breaking change] The
MIToS.Utils.Scriptsmodule and the MIToS scripts have been moved to their package at MIToS_Scripts.jl. Therefore, theMIToS.Utils.Scriptsmodule is no longer exported. This allows for a reduction in the number of MIToS dependencies, and improved load time.
- Julia
Published by github-actions[bot] over 1 year ago
MIToS - v2.22.0
MIToS v2.22.0
This versions introduces several breaking changes to improve the usability of the
Information module. The main changes are:
[Breaking change] The
Informationmodule deprecates theCountstype in favor of the newFrequenciestype. The new type as the same signature and behavior as the old one.[Breaking change] The
countfunction on sequences has been deprecated in favor of thefrequenciesfunction, which has the same signature and behavior as the old one.[Breaking change] The
count!function is deprecated in favor offrequencies!. 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 byfrequencies!(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 byprobabilities!(table, seqs..., weights=weights, pseudocounts=pseudocounts, pseudofrequencies=pseudofrequencies).[Breaking change] The
Informationhas deprecated theentropymethod onFrequenciesandProbabilitiesin favor of theshannon_entropyfunction. The definition of the base is now done using thebasekeyword argument. As an example of migration,entropy(p, 2)should be replaced byshannon_entropy(p, base=2).[Breaking change] The
marginal_entropymethods based on positional arguments are deprecated in favor of a method relying on themarginandbasekeyword arguments. As an example of migration,marginal_entropy(p, 2, 2.0)should be replaced bymarginal_entropy(p, margin=2, base=2.0).[Breaking change] The
mutual_informationmethod based on positional arguments is deprecated in favor of a method relying on thebasekeyword argument. As an example of migration,mutual_information(p, 2)should be replaced bymutual_information(p, base=2).[Breaking change] The
mapcolpairfreq!andmapseqpairfreq!functions now uses the booleanusediagonalkeyword argument to indicate if the function should be applied to the diagonal elements of the matrix (the default istrue). Before, this was done passingVal{true}orVal{false}as the last positional argument.The
mapcolfreq!,mapseqfreq!,mapcolpairfreq!, andmapseqpairfreq!methods using keyword arguments, now pass the extra keyword arguments to the mapped function.The
Informationmodule now exports themapfreqfunction that offers a more high-level interface to themapcolfreq!,mapseqfreq!,mapcolpairfreq!, andmapseqpairfreq!functions. This function allows the user to map a function to the residue frequencies or probabilities of the columns or sequences of an MSA. Whenrank = 2, the function is applied to pairs of sequences or columns.The
Informationmodule now exports methods of theshannon_entropy,kullback_leibler,mutual_information, andnormalized_mutual_informationfunctions that take anAbstractArray{Residue}as input, e.g. an MSA. Those methods use themapfreqfunction under the hood to ease the calculation of the information measures on MSAs.The
frequencies!,frequencies,probabilities!, andprobabilitiesfunctions now accept arrays ofResidues of any dimension. Therefore, there is no need to use thevecfunction to convert the arrays to vectors.The
MSAmodule now exports theWeightTypeunion type to representweights.
- Julia
Published by github-actions[bot] over 1 year ago
MIToS - v2.16.0
MIToS v2.16.0
Merged pull requests: - Formatting -> Format (#74) (@timholy) - Parsing: fix Stockholm for Clustal Omega output (#75) (@timholy) - Adding AlphaFoldDB file (#76) (@LouiseB25) - Revert "CI: Do not test Julia 1.0" (#78) (@timholy)
Closed issues: - downloadpfam fails for full alignments (#73)
- Julia
Published by github-actions[bot] over 1 year ago
MIToS - v2.6.0
MIToS v2.6.0
Closed issues: - 404 error from function 'getpdbdescription' (#59)
Merged pull requests: - CompatHelper: bump compat for "DataStructures" to "0.18" (#55) (@github-actions[bot]) - CompatHelper: bump compat for "HTTP" to "0.9" (#56) (@github-actions[bot]) - CompatHelper: bump compat for "StaticArrays" to "1.0" (#57) (@github-actions[bot])
- Julia
Published by github-actions[bot] almost 5 years ago
MIToS - MIToS 2.3.3
Solve minor bug with empty file reading
- Julia
Published by diegozea about 7 years ago
MIToS - MIToS 2.3.2
Solve gaussdca bug with Julia 1.0 and Windows
- Julia
Published by diegozea about 7 years ago
MIToS - MIToS 2.3.1
Solve gaussdca bug with Julia 1.0
- Julia
Published by diegozea about 7 years ago
MIToS - MIToS 2.3.0
MIToS v2.3 requires Julia v0.7 or v1.0. This release drops Julia 0.6 support.
Formatting.jlis used in place ofFormat.jl.SIFTS.getreturns the desired object ormissinginstead ofNullables.
- Julia
Published by diegozea about 7 years ago
MIToS - MIToS 2.2.0
PIRFileFormatis included to read and write alignments in PIR/NBRF format.Utils.Formatwas renamed toUtils.FileFormatHTTP.jlis used in place ofFTPClient.jland the deprecatedRequests.jlinUtils.download_fileto download files.Format.jlis used in place ofFormatting.jlSolve bug in the printing of matrices of
Residues usingFileFormats.
- Julia
Published by diegozea over 7 years ago
MIToS - MIToS 2.1.2
FTPClient.jlis used inUtils.download_fileto download files from FTP.CodecZlib.jlis used in place ofGZip.jlspeeding up the parsing of compressed files.Improvements in MSA and PDB parsing speed.
Improvement in
MSA.percentidentityspeed.Information.gaussdcanow uses Julia'sserializeanddeserializeinstead ofJLD.
- Julia
Published by diegozea over 7 years ago
MIToS - MIToS 2.1.1
The Conservation.jl script was added.
- Julia
Published by diegozea about 8 years ago
MIToS - MIToS 2.0
MIToS 2.0 is the first MIToS version with Julia 0.5 support (It drops Julia 0.4 support). MIToS was slightly redesigned to take advantage of the new Julia capabilities. As a consequence, this version introduces several breaking changes and new features.
- Julia
Published by diegozea over 8 years ago