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MIToS.jl Release Notes

Changes from v2.22.0 to 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 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.

Changes from v2.21.0 to v2.22.0

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.

Changes from v2.20.0 to v2.21.0

  • [Breaking change] The buslje09 and BLMI functions from the Information module does not longer accept a filename and a file format as arguments. You should explicitly read the MSA using the read_file function and then run the buslje09 or BLMI functions on the returned MSA object. As an example of migration, buslje09("msa.sto", "Stockholm") should be replaced by buslje09(read_file("msa.sto", Stockholm)).

Changes from v2.19.0 to v2.20.0

  • [Breaking change] The PDB module has deprecated residues and @residues in favor of the select_residues function that uses keyword arguments. So, residues(pdb, "1", "A", "ATOM", All) or @residues pdb "1" "A" "ATOM" All should be replaced by select_residues(pdb, model="1", chain="A", group="ATOM").

  • [Breaking change] The PDB module has deprecated atoms and @atoms in favor of the select_atoms function that uses keyword arguments. So, atoms(pdb, "1", "A", "ATOM", All, "CA") or @atoms pdb "1" "A" "ATOM" All "CA" should be replaced by select_atoms(pdb, model="1", chain="A", group="ATOM", atom="CA").

  • [Breaking change] The PDB module has deprecated the methods of the isresidue and residuesdict functions that rely on positional arguments in favor of the keyword arguments. So, isresidue(pdb, "1", "A", "ATOM", "10") should be replaced by isresidue(pdb, model="1", chain="A", group="ATOM", residue="10"). Similarly, residuesdict(pdb, "1", "A", "ATOM", All) should be replaced by residuesdict(pdb, model="1", chain="A", group="ATOM").

Changes from v2.18.0 to v2.19.0

  • [Breaking change] The shuffle and shuffle! functions are deprecated in favor of the shuffle_msa and shuffle_msa! functions. The new functions take dims and fixedgaps as keyword arguments instead of taking them as positional ones. The new functions add a last positional argument to allow the selection of specific sequences or columns to shuffle. Also, it adds the fixed_reference keyword argument to keep the residues in the reference sequence fixed during the shuffling. As an example of migration, shuffle!(msa, 1, false) should be replaced by shuffle_msa!(msa, dims=1, fixedgaps=false).

Changes from v2.17.0 to v2.18.0

  • [Breaking change] The read, parse, write, and print functions for different FileFormats have been deprecated in favor of the read_file, parse_file, write_file, and print_file functions. The new functions keep the same signature and behavior as the old ones.

Changes from v2.16.0 to v2.17.0

  • [Breaking change] The download_file now uses the Downloads.jl module instead of HTTP.jl. Therefore, the download_file function now accepts the Downloads.download keyword arguments. In particular, the redirect and proxy keyword arguments are no longer needed.

  • The MSA module now exports the A2M and A3M file formats, to allow reading and writing MSA files in these formats.

Changes from v2.15.0 to v2.16.0

MIToS v2.16.0 drops support for Julia 1.0. This release requires Julia 1.6 or higher.

  • [Breaking change] The transpose function is now deprecated for MSA and sequences (AbstractAlignedObjects). Use permutedims instead.

  • [Breaking change] MIToS is now using JSON3.jl instead of JSON.jl. That change the returned type of getpdbdescription from Dict{String, Any} to JSON3.Object. Since the JSON3.Object supports the Dict interface, the change should not cause any issues. If you want to convert the returned JSON3.Object to a Dict{String, Any} you can use the MIToS.PDB.JSON3.copy function.

  • The PDB module now defines the query_alphafolddb and download_alphafold_structure functions to query the AlphaFold Protein Structure Database and download the predicted structures.

  • This version solves a bug when reading MSA files with | in the sequence names.

  • MIToS is now using Format.jl instead of Formatting.jl.

Changes from v2.14.1 to v2.15.0

  • The MSA module now exports the rename_sequences! and rename_sequences functions to rename the sequences of an MSA object.

Changes from v2.14.0 to v2.14.1

  • The modelled_sequences function now returns only the selected chains, therefore avoid the inclusion of empty sequences in the output.

Changes from v2.13.1 to v2.14.0

  • The MSA now defines join for MSA objects, allowing to join or merge two AnnotationMultipleSequenceAlignment objects based on a list of matching sequences or columns.

  • The MSA module now defines hcat and vcat for MSA objects, taking care of sequence and column names, and MSA annotations.

  • The MSA now exports the sequencename_iterator and columnname_iterator functions to return an iterator over the sequence or column names of an MSA.

  • The MSA now exports the sequence_index and column_index functions to return the integer position of a sequence or column name in an MSA.

  • merge and merge! are now defined for Annotations objects in the MSA module.

Changes from v2.13.0 to v2.13.1

  • The PDB module can now parse the 66-character width columns of the PDB files created by Foldseek. These structures contain only the alpha carbons and do not have the column determining the element symbol.

Changes from v2.12.0 to v2.13.0

  • The PDB module now includes the modelled_sequences function, allowing extraction of protein sequences from a specified structure.

  • The PDB module exports the is_aminoacid function to determine whether a PDBResidue represents an amino acid residue. This function is utilized by the modelled_sequences function.

  • The Utils module now exports the THREE2ONE constant, which is a dictionary mapping three-letter amino acid residue codes to their corresponding one-letter codes.

Changes from v2.11.1 to v2.12.0

  • The downloadsifts function now downloads the SIFTS files from the PDBe HTTPS server instead of the previous FTP server. This improves error handling during the download process, making it more robust by relying on the download_file function. If you prefer the previous behavior, you can set the new keyword argument source to "ftp".

  • It resolves an issue with the representation of Multiple Sequence Alignments and ContingencyTables in the show methods by always using explicit MIME types.

  • [Breaking change] The show methods that accept only two elements without an explicit MIME type are now deprecated.

Changes from v2.11.0 to v2.11.1

  • MIToS now checks the magic number of gzip files immediately after download. If the gzip file does not have the correct header, MIToS will attempt to download it again. In Julia versions below 1.2, it will retry the download once. In Julia 1.2 or higher, it will retry the download five times, using an ExponentialBackOff.

Changes from v2.10.0 to v2.11.0

  • [breaking change] getCA returns missing if a PDBResidue has no CA atom (before it was an AssertionError).

Changes from v2.9.0 to v2.10.0

  • [breaking change] downloadsifts now uses Base.download instead of download_file as HTTP (1.7 or lower) doesn't support FTP. Because of that, it doesn't accept keywords argument as download_file besides filename.

  • MIToS now supports HTTP 1.0 and has migrated from using HTTP.request to using HTTP.download for MIToS.Utils.download_file dropping support on HTTP 0.8. Thanks, @kool7d!

  • The downloadpfam function now uses the InterPro API, as the Pfam website has been discontinued. Thanks, @timholy!

  • The downloadpfam function now has an alignment keyword argument for choosing which Pfam alignment download. The options are "full" (the default), "seed" and "uniprot".

  • MIToS switched to GitHub Actions for CI. Thanks, @timholy!

Changes from v2.8.6 to v2.9.0

  • New matches keyword argument in the superimpose function to determine the residues to be aligned. Thanks, @timholy!

Changes from v2.8.1 to v2.8.6

  • You can pass keyword arguments from downloadsifts to download_file.

Changes from v2.8.1 to v2.8.5

  • Fix bugs when concatenating concatenated MSAs using hcat.

Changes from v2.8.1 to v2.8.4

  • Ensure that gaussdca use the correct project file.

Changes from v2.8.1 to v2.8.3

  • Increase PairwiseListMatrices required version.

  • Fix bugs when concatenating concatenated MSAs using hcat.

Changes from v2.8.0 to v2.8.1

Fix bug when reading hcat generated MSA in Stockholm format.

Changes from v2.7.0 to v2.8.0

Multiple bug fixes and improvements related to getindex and hcat.

  • [breaking change] MSA getindex can now change the order of the columns in an AnnotatedMultipleSequenceAlignment.

  • [breaking change] convert to MSA and sequence objects is now deprecated; use the corresponding constructor.

  • gethcatmapping to get the mapping to the concatenated MSAs.

Changes from v2.6.1 to v2.7.0

  • [breaking change] MSA getindex with : or arrays now return an object of the same type. The annotations of an AnnotatedMultipleSequenceAlignment are modified according to the selection.

  • [breaking change] MSA getindex can now change the order of the sequences in an AnnotatedMultipleSequenceAlignment.

  • It adds hcat support for MSA objects, taking care of the MSA annotations.

Changes from v2.6.0 to v2.6.1

  • download_file and other download... functions now use the proxy settings declared with the HTTP_PROXY and HTTP_PROXY environment variables.

Changes from v2.5.0 to v2.6.0

  • The RESTful API of PDB has changed, and the Legacy Fetch API Web Service was shut down on December 9th, 2020. To adapt to the new changes, PDBMLHeader has been deprecated, and the downloadpdbheader and getpdbdescription functions now return different objects.

Changes from v2.4.0 to v2.5.0

MIToS v2.5.0 drops support for Julia 0.7 and adds support for Julia 1.5 and includes several bug fixes.

  • Cookbook section added to the docs using Literate

  • The SIFTS module now includes the dbSCOP2 and dbSCOP2B databases.

  • siftsmapping now returns an OrderedDict instead of a Dict.

  • msacolumn2pdbresidue now return an OrderedDict instead of a Dict.

Changes from v2.3.0 to v2.4.0

MIToS v2.4 uses Project.toml and includes several bug fixes.

  • The SIFTS module includes the dbEnsembl database and warns again about unused databases.

Changes from v2.2.0 to v2.3.0

MIToS v2.3 requires Julia v0.7 or v1.0. This release drops Julia 0.6 support.

  • Formatting.jl is used in place of Format.jl.

  • SIFTS.get returns the desired object or missing instead of Nullables.

  • SIFTS function doesn't warn about unused databases.

Julia 0.7/1.0 deprecations

  • bits was deprecated to bitstring.

  • ' and .' are deprecated for alignments and sequences, use transpose or permutedims instead. ctranspose is not longer available for matrices of Residues.

Changes from v2.1.2 to v2.2

  • PIR FileFormat is included to read and write alignments in PIR/NBRF format.

  • Utils.Format was renamed to Utils.FileFormat.

  • HTTP.jl is used in place of FTPClient.jl and the deprecated Requests.jl in Utils.download_file to download files.

  • Format.jl is used in place of Formatting.jl.

  • Solve bug in the printing of matrices of Residues using FileFormats.

Changes from v2.1.1 to v2.1.2

  • FTPClient.jl is used in Utils.download_file to download files from FTP.

  • CodecZlib.jl is used in place of GZip.jl speeding up the parsing of compressed files.

  • Improvements in MSA and PDB parsing speed.

  • Improvement in MSA.percentidentity speed.

  • Information.gaussdca now uses Julia's serialize and deserialize instead of JLD.

  • ROCAnalysis.jl is not longer a dependency and it's now used with @require from Requires.jl. To use the AUC function you need to do using ROCAnalysis.

Changes from v2.1 to v2.1.1

  • The script Conservation.jl was added to measure residue conservation of MSA columns.

  • The script SplitStockholm.jl now has a progress bar thanks to Ellis Valentiner @ellisvalentiner.

Changes from v2.0 to v2.1

MIToS v2.1 requires Julia v0.6. This release drops Julia 0.5 support.

  • get_n_words(... doesn't remove the last newline character, use get_n_words(chomp(... to get the previous behaviour.

Changes from v1.2.3 to v2.0

MIToS 2.0 is the first MIToS version with Julia 0.5 support (It drops Julia 0.4 support). The last Julia version introduces new awesome features like native multi-threading support, fast anonymous functions, generator expressions and more. Also, the Julia package ecosystem has grown. So, MIToS was slightly redesigned to take advantage of the new Julia capabilities. As a consequence, this version introduces several breaking changes and new features.

Utils module

  • deleteitems!(vector::Vector, items) is deprecated in favor of filter!(x -> x ∉ items, vector).

  • All is used instead of MIToS 1.0 "all" or "*", because it's possible to dispatch on it.

Vectorized queries are deprecated

Previous version of Utils included methods and types in order to overcome the performance cost of functional programing in previous Julia versions. In particular, vectorized queries were performed using subtypes of AbstractTest, in particular the TestTypes Is and In and the TestOperation Not. This types were used as argument to the query methods capture and isobject. This operation were fused and vectorized with the methods: findobjects, collectobjects and collectcaptures. All these functions and types are deprecated in MIToS 2.0. Functional programming in Julia 0.5 is fast, so these methods can be easily replace by Julia higher order functions like find and filter and lambda expressions (anonymous functions).

MSA module

  • Residue is now encoded as Int instead of being encoded as UInt8, allowing faster indexation using Int(res::Residue). More memory is used, since the residues are encoded using 32 or 64 bits instead of 8 bits.

  • XAA is now used to indicate unknown, ambiguous and non standard residues instead of GAP.

  • Conversions to and from UInt8 aren't supported now.

  • More Base methods are extended to work with Residue: bits, zero, one and isvalid.

  • empty(Annotations) was deprecated, use Annotations() instead.

  • msa["seq_name",:] now returns a NamedArray{Residue,1} instead of an aligned sequence, use getsequence(msa,"seqname") to get an aligned sequence with annotations.

  • The names function was replaced by the sequencenames function. A columnnames function was also added.

  • Aligned sequences don't drop dimensions, so there are matrices instead of vectors. You can use vec(...) or squeeze(...,1) to get a vector instead of the matrix.

  • Indexing MSA objects with only one string is deprecated, use msa["seqname",:] instead of msa["seqname"].

  • empty! doesn't take MSA objects anymore.

  • asciisequence was replaced by stringsequence.

  • deletenotalphabetsequences and the parse/read keyword argument checkalphabet are deprecated since MIToS 2.0 uses Residue('X') to represent residues outside the alphabet. You can use filtersequences!(msa, vec(mapslices(seq -> !in(XAA, seq), msa, 2))) to delete sequences with unknown, ambiguous or non standard residues.

  • parse/read and MSA file returns an AnnotatedMultipleSequenceAlignment by default.

  • shuffle_...columnwise! and shuffle_...sequencewise! functions were deprecated in favor of shuffle! and shuffle functions.

  • SequenceClusters was renamed to Clusters.

  • Residue alphabet types were added. All alphabet types are subtypes of ResidueAlphabet. In particular, three types are exported: GappedAlphabet, UngappedAlphabet and ReducedAlphabet. The last type allows the creation of custom reduced alphabets.

  • In order to keep the sequence name, AlignedSequence and AnnotatedAlignedSequence are now matrices instead of vectors.

PDB module

  • The keyword argument format of downloadpdb should be a type (PDBFile or PDBML) instead of a string (pdb or xml) as in MIToS 1.0.

  • read and parse now has the occupancyfilter keyword argument.

  • read and parse now has the label keyword argument for PDBML files.

  • residues, àtoms and similiar functions don't take vectors or sets anymore. Use an anonymous function instead, e.g.: x -> x in set_of_residue_numbers.

  • The functions isresidue, isatom and residuepairsmatrix were added.

SIFTS module

  • The get function has a more complex signature for SIFTSResidues to make simpler the access of data.

  • find, filter and filter now takes a database type as a third parameter when a vector of SIFTSResidues is the second parameter. It allows to use a function that directly operates over the database type if it's available.

  • SIFTSResidues now also store secondary structure data in the sscode and ssname fields.

Information module

  • ResidueProbability and ResidueCount were deprecated in favor of ContingencyTable. Probabilities and Counts were added as wrappers of ContingencyTable to allow dispach in a some functions, e.g. entropy.

  • The last parameter of contingency tables is now a subtype of ResidueAlphabet instead of a Bool, i.e.: UngappedAlphabet, GappedAlphabet or ReducedAlphabet.

  • Creation of empty contingecy tables chaged. e.g. zeros(ResidueProbability{Float64, 2, false}) changed to ContingencyTable(Float64, Val{2}, UngappedAlphabet()) and ResidueProbability{Float64, 2, false}() changed to ContingencyTable{Float64, 2, UngappedAlphabet}(UngappedAlphabet()).

  • count! and probabilities! signatures changed. The first argument is alway a ContingencyTable, the second positional argument a clustering weight object (use NoClustering() to skip it), the third positional argument is a pseudocount object (use NoPseudocount() to avoid the use of pseudocounts) and probabilities! takes also a Pseudofrequencies object (use NoPseudofrequencies() to avoid pseudofrequencies). The last positional arguments are the vector of residues used to fill the contingency table.

  • count and probabilities now takes the sequences as only positional arguments. The output is always a table of Float64. Both functions take the keyword arguments alphabet, weights and pseudocounts. probabilities also has a pseudofrequencies keyword argument.

  • apply_pseudofrequencies! changed its signature. Now it takes a ContingencyTable and a Pseudofrequencies object.

  • The function blosum_pseudofrequencies! was deprecated in favor of introducing a BLOSUM_Pseudofrequencies type as subtype of Pseudofrequencies to be used in probabilities, probabilities! and apply_pseudofrequencies!.

  • Because higher-order function are fast in Julia 0.5, measure types (i.e. subtypes of AbstractMeasure) were deprecated in favor of functions. In particular, MutualInformation was replaced with the mutual_information function, MutualInformationOverEntropy was replaced with normalized_mutual_information, KullbackLeibler was replaced with kullback_leibler and Entropy was replaced with entropy.

  • The functions estimate, estimate_on_marginal , estimateincolumns and estimateinsequences were deprecated because measure types are not longer used.

  • estimate_on_marginal(Entropy... was deprecated in favor of the marginal_entropy function.

  • estimateincolumns and estimateinsequences were deprecated in favor of mapcolfreq!, mapseqfreq!, mapcolpairfreq! and mapseqpairfreq.

  • Keyword argument usegaps is deprecated in buslje09 and BLMI in favor of alphabet.

  • cumulative function was added to calculate cumulative MI (cMI).

Changes from v1.1 to v1.2.2

  • using Plots to use plot with AbstractVector{PDBResidue} to visualize coordinates of the C alpha of each residue.

  • Re-exports swap! from IndexedArrays.jl.

  • [breaking change] Distances.jl now uses --inter instead of --intra.

  • docs and cookbook are now in MIToSDocumentation

Changes from v1.0 to v1.1

  • RecipesBase is used to generate plot recipes for MIToS’ objects. MSA objects can be visualized using Plots (thanks to Thomas Breloff @tbreloff ).

  • Functions to perform structural superimposition were added to the PDB module (thanks to Jorge Fernández de Cossío Díaz @cosio ) : center!, kabsch, rmsd.

  • The PDB module adds the following functions to make easier structural comparison: getCA, CAmatrix, coordinatesmatrix, centeredcoordinates, centeredresidues, change_coordinates, superimpose, mean_coordinates and rmsf.

  • When PDB or PDBML files are being parsed, It’s possible to indicate if only atoms with the best occupancy should be loaded (occupancyfilter=true, false by default).

  • When PDBML files are being parsed, is possible to used the new label keyword argument to indicate if "auth" (false) or "label" (true) attributes should be used.

  • bestoccupancy! was deprecated in favor of bestoccupancy.

  • The MSA module export the function percentsimilarity to calculate the similarity percent between aligned sequences.

  • msacolumn2pdbresidue has two new keyword arguments, strict and checkpdbname, to perform extra tests during the mapping between PDB and MSA residues.

  • msacolumn2pdbresidue has a new missings keyword argument to indicate if missing residues should be included in the mapping (default: true).

  • The MSA now exports the residue2three and three2residue function to convert Residues to and from their three letter names.

  • The MSA module now exports sequencepairsmatrix, columnpairsmatrix, columnlabels, and sequencelabels to help in the construction of matrices for MSA sequences or columns pairwise comparisons.

  • The Information module, if GaussDCA is installed, allows to call its gDCA function from MIToS through the gaussdca function.

  • The Information module now exports the KullbackLeibler measure.

  • Now is possible to print and write PDBResidues as PDBFiles.

  • The function proximitymean now has a keyword argument include to indicate if the residue score should be included in the mean.

  • The module Scripts inside the Utils module has a new function readorparse to help parsing STDIN in MIToS’ scripts.

MIToS v1.1 also includes several bug fixes, some performance improvements and a more complete documentation.

Changes from v0.1 to v1.0

  • Pfam module for working with Pfam alignments and useful parameter optimization functions (i.e. AUC).

  • [breaking change] The Clustering module was deleted and its functions moved to the MSA module.

  • MSA uses ClusteringResult from the Clustering.jl package instead of AbstractClusters.

    • Clusters was renamed to SequenceClusters

    • MSA adds the counts and assignments functions from the Clustering.jl interface.

    • [breaking change] The getnclusters function is now nclusters in the Clutering module.

  • [breaking change] All the MSA ...percentage functions were renamed to ...fraction and percent... functions now return real percentages (not fractions) values. Functions taking identity thresholds, now also take real percentages (values between 0.0 and 100.0).

  • [breaking change] Script command line arguments changed to: define the number of workers, use STDIN and STDOUT (pipelines), get better output names, use real flag arguments.

  • InformationMeasure renamed to AbstractMeasure.

  • New functions added to MSA module.

    • annotations, names.

    • meanpercentidentity allows fast estimation of the mean percent identity between the sequences of a MSA.

  • New function and type added to Information module.

    • cumulative to calculate cMI (cumulative mutual information) and similar cumulative scores.

    • KullbackLeibler to estimate conservation.

  • proximitymean is defined in the PDB module to calculate pMI (proximity mutual information) and other proximity scores.

  • contact and distance have a vectorized form to create contact/distance maps.

  • NCol file annotation with the number of columns in the original MSA.

  • BLMI has lambda as a keyword argument for using additive smoothing.

  • BLMI and buslje09 accepts samples=0 to avoid the Z score estimation.

  • read/parse added the keyword argument checkalphabet for deleting sequences with non standard amino acids.

  • read/parse added the keyword argument keepinserts for keep insert columns (It creates an Aligned column annotation).

MIToS v1.0 also includes several bug fixes and a more complete documentation.