Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.4.7 - 2021-09-28

Added

• TraceAligner, Trace and Traces classes to pyhmmer.plan7 to get tracebacks after aligning several sequences against an HMM.

• pyhmmer.hmmalign function with the same features as the hmmalign binary from HMMER3.

• Support for out-of-band pickling in easel.Vector and easel.Matrix.

Changed

• Allow creating an empty Vector or Matrix by calling their constructor without arguments.

Fixed

• Potential unreported exceptions in plan7.OptimizedProfile.write and several plan7.SSIWriter methods.

v0.4.6 - 2021-09-10

Added

• pickle protocol for easel.Alphabet, easel.Bitfield, easel.KeyHash, easel.Vector, easel.Matrix and plan7.HMM.

• taxonomy_id and residue_markups properties to easel.Sequence.

• sum_score property to plan7.Hit.

• plan7.EvalueParameters class to expose the e-value parameters of a plan7.HMM or a plan7.Profile.

• Equality checks and slicing for easel.Matrix and easel.Vector.

• Support for creating and manipulating zero-sized easel matrices and vectors.

• plan7.Cutoffs class to expose the Pfam score cutoffs of a plan7.HMM or a plan7.Profile.

• Keyword arguments to configure E-value thresholds when creating a plan7.Pipeline object.

• Support for using model-specific thresholding options in plan7.Pipeline.

Changed

• Use the replace error handler when decoding error messages to skip potential decoding issues when already building an exception.

• Improve pyhmmer.hmmer to ensure background threads exit on a KeyboardInterrupt.

• easel.VectorU8.__eq__ accepts any object implementing the buffer protocol.

• plan7.HMM.creation_time now takes and returns a datetime.datetime object, assuming the field is only ever set with asctime.

• Refactor easel.Vector and easel.Matrix and mark exposed memory as C-contiguous.

Fixed

• easel.Alphabet not reporting potential allocation errors.

• Potential buffer overflow in easel.Matrix and easel.Vector when calling __init__ more than once.

v0.4.5 - 2021-07-19

Added

• OptimizedProfile.convert method to configure an optimized profile from a Profile without reallocating a new P7_OPROFILE struct.

Changed

• Rewrite the plan7.Pipeline search loop to avoid reacquiring the GIL between reference sequences.

• Require the reference sequences to be stored in a collection (instead of an iterable) when passing them to the search_hmm, search_msa and search_seq methods of plan7.Pipeline.

• Avoid reallocating a new OptimizedProfile every time a new HMM is passed to Pipeline.search_hmm.

• Relax the GIL while sorting and thresholding TopHits in Pipeline search methods.

v0.4.4 - 2021-07-07

Added

• ignore_gaps parameter to pyhmmer.plan7.SequenceFile, allowing to skip the gap characters when reading a sequence from an ungapped format.

• __sizeof__ implementation for some

• Dedicated check for sequence length before running the platform-specific code in pyhmmer.plan7.Pipeline.

Fixed

• Score system not being set in pyhmmer.plan7.Builder.build_msa.

• Alphabet not being checked after the first sequence in Pipeline search and scan methods.

v0.4.3 - 2021-07-03

Fixed

• File object wrappers not reporting exceptions raised when seeking on OSX/BSD platforms.

v0.4.2 - 2021-06-20

Added

• pyhmmer.easel.Randomness class exposing a deterministic random number generator.

• pyhmmer.plan7.Builder.randomness and pyhmmer.plan7.Pipeline.randomness attributes exposing the internal random number generator used by each object.

• pyhmmer.plan7.Hit.best_domain property mapping to the highest scoring domain of a hit.

• pyhmmer.plan7.OptimizedProfile.rbv property exposing match scores.

• pyhmmer.plan7.Domain.pvalue and pyhmmer.plan7.Hit.pvalue reporting the p-value for a domain or hit bitscore.

Fixed

• Dimensions of the pyhmmer.plan7.OptimizedProfile.sbv matrix not being properly set.

v0.4.1 - 2021-06-06

Fixed

• Main buffer not being freed in MatrixF.__dealloc__ and MatrixU8.__dealloc__ when created without owner.

Added

• Additional configuration values for pyhmmer.plan7.Pipeline as both constructor arguments and mutable properties.

• consensus, consensus_structure and offsets properties to pyhmmer.plan7.Profile objects.

Changed

• Make OptimizedProfile.ssv_filter check the alphabet of the given sequence.

v0.4.0 - 2021-06-05 - YANKED

Added

• Linear algebra primitives to expose 1D (Vector) and 2D (Matrix) contiguous buffers containing numerical values to pyhmmer.easel.

• Documentation for the Z and domZ parameters of the pyhmmer.plan7.Pipeline constructor.

• pyhmmer.errors.AlphabetMismatch exception deriving from ValueError to specifically report mismatching Easel alphabets where applicable.

• scale and normalize methods to pyhmmer.plan7.HMM objects.

• Property to access pyhmmer.plan7.Background residue frequencies as a VectorF object.

• Property to access pyhmmer.plan7.HMM mean residue composition as a VectorF object.

• Property to access pyhmmer.plan7.HMM probabilities and emissions as MatrixF objects.

• ssv_filter methods to pyhmmer.plan7.OptimizedProfile to get the SSV filter score of the profile for a given sequence.

• Several additional properties to access the pyhmmer.plan7.OptimizedProfile internals.

Removed

• Unused report_e parameter of pyhmmer.plan7.Pipeline constructor.

• pyhmmer.plan7.TopHits.clear method which could lead to segfault if it was called while a Hit is being held.

Changed

• Multithreaded loop in pyhmmer.hmmer to reduce memory consumption while still yielding hits in order.

• pyhmmer.easel.DigitalSequence.sequence property is now a VectorU8.

Fixed

• Type annotations in pyhmmer.hmmer.

• Potential double free in pyhmmer.plan7.HMM.command_line property setter.

• Minor floating-point precision issues in pyhmmer.plan7.Builder constructor.

• Segfault in TextMSA.digitize caused by esl_msa_Copy not digitizing on-the-fly like esl_sq_Copy.

• Exceptions not being raised in some methods of pyhmmer.plan7.Profile and pyhmmer.plan7.TopHits.

v0.3.1 - 2021-05-08

Added

• Pipeline.scan_seq method to query a database of profiles with one or more sequences.

• transition_probabilities, match_emissions, insert_emissions properties to the HMM class, providing access to the numerical parameters of the HMM.

• consensus_structure and consensus_accessibility properties to the HMM class to get consensus lines from the source alignment if the HMM was created from a MSA.

• nseq and nseq_effective properties to the HMM class to get the number of training sequences and effective sequences used to build the HMM.

Changed

• HMM.checksum is now None if the p7H_CHKSUM flag is not set.

• Builder methods will now record sys.argv when creating a HMM.

Fixed

• HMM.write(..., binary=False) crashing on HMMs without a consensus line. (#5). Fixed upstream in (EddyRivasLab/HMMER#236).

• Pipeline.reset mishandling the Z and domZ values if those were detected from the number of targets.

• pyhmmer.hmmer functions will not block until all results have been collected anymore when run in multithreaded mode.

v0.3.0 - 2021-03-11

Added

• easel.MSAFile to read from a file containing

• accession, author, name and description properties to easel.MSA objects.

• plan7.Builder.build_msa to build a pHMM from a sequence alignment.

• Additional methods to easel.KeyHash, allowing to use it as a dict/set hybrid.

• Sequence.write and MSA.write methods to format a sequence or an alignment to a file handle.

• plan7.TopHist.to_msa method to convert all the top hits of a query against a database into a multiple sequence alignment.

• easel.MSA.sequences attribute to access individual sequences of an alignment using the collections.abc.Sequence interface.

• easel.DigitalMSA.textize method to convert a multiple sequence alignment in digital mode to its text-mode counterpart.

• Read-only name, accession and description properties to plan7.Profile showing attributes inherited from the HMM it was configured with.

• plan7.HMM.consensus property, allowing to access the consensus sequence of a pHMM.

• plan7.HMM equality implementation, using zero tolerance.

• plan7.Pipeline.search_msa to query a MSA against a sequence database.

• easel.Sequence.reverse_complement method allowing to reverse-complement inplace or to build a copy.

• errors.AlphabetMismatch exception for use in cases where an alphabet is expected but not matched by the input.

• hmmer.nhmmer function with the same behaviour as hmmer.phmmer, except it expects inputs with a DNA alphabet.

Fixed

• plan7.Builder.copy not copying some parameters correctly, causing pyhmmer.hmmer.phmmer to give inconsistent results in multithreaded mode.

• easel.Bitfield not properly handling index overflows.

• Documentation not rendering for the __init__ method of all classes.

Changed

• plan7.Builder gap-open and gap-extend probabilities are now set on instantiation and depend on the alphabet type.

• Constructors for easel.TextMSA and easel.DigitalMSA, which can now be given an iterable of easel.Sequence objects to store in the alignment.

Removed

• Unimplemented easel.SequenceFile.fetch and easel.SequenceFile.fetchinto methods.

v0.2.2 - 2021-03-04

Fixed

• Linking issues on OSX caused by aggressive stripping of intermediate libraries.

• plan7.Builder RNG not reseeding between different HMMs.

v0.2.1 - 2021-01-29

Added

• pyhmmer.plan7.HMM.checksum property to get the 32-bit checksum of an HMM.

v0.2.0 - 2021-01-21

Added

• pyhmmer.plan7.Builder class to handle building a HMM from a sequence.

• Pipeline.search_seq to query a sequence against a sequence database.

• psutil dependency to detect the most efficient thread count for hmmsearch based on the number of physical CPUs.

• pyhmmer.hmmer.phmmer function to run a search of query sequences against a sequence database.

Changed

• Pipeline.search was renamed to Pipeline.search_hmm for disambiguation.

• libeasel.random sequences do not require the GIL anymore.

• Public API now have proper signature annotations.

Fixed

• Inaccurate exception messages in Pipeline.search_hmm.

• Unneeded RNG reallocation, replaced with re-initialisation where possible.

• SequenceFile.__next__ not working after being set in digital mode.

• sequences argument of hmmsearch now only requires a typing.Collection[DigitalSequence] instead of a typing.Collection[Sequence] (not more __getitem__ needed).

Removed

• hits argument to Pipeline.search_hmm to reduce risk of issues with TopHits reuse.

• Broken alignment coordinates on Domain classes.

v0.1.4 - 2021-01-15

Added

• DigitalSequence.textize to convert a digital sequence to a text sequence.

• DigitalSequence.__init__ method allowing to create a digital sequence from any object implementing the buffer protocol.

• Alignment.hmm_accession property to retrieve the accession of the HMM in an alignment.

v0.1.3 - 2021-01-08

Fixed

• Compilation issues in OSX-specific Cython code.

v0.1.2 - 2021-01-07

Fixed

• Required Cython files not being included in source distribution.

v0.1.1 - 2020-12-02

Fixed

• HMMFile calling file.peek without arguments, causing it to crash when passed some types, e.g. gzip.GzipFile.

• HMMFile failing to work with PyPy file objects because of a bug with their implementation of readinto.

• C/Python file object implementation using strcpy instead of memcpy, causing issues when null bytes were read.

v0.1.0 - 2020-12-01

Initial beta release.

Fixed

• TextSequence uses the sequence argument it’s given on instantiation.

• Segmentation fault in Sequence.__eq__ caused by implicit type conversion.

• Segmentation fault on SequenceFile.read failure.

• Missing type annotations for the pyhmmer.easel module.

v0.1.0-a5 - 2020-11-28

Added

• Sequence.__len__ magic method so that len(seq) returns the number of letters in seq.

• Python file-handle support when opening an pyhmmer.plan7.HMMFile.

• Context manager protocol to pyhmmer.easel.SSIWriter.

• Type annotations for pyhmmer.easel.SSIWriter.

• add_alias to pyhmmer.easel.SSIWriter.

• write method to pyhmmer.plan7.OptimizedProfile to write an optimized profile in binary format.

• offsets property to interact with the disk offsets of a pyhmmer.plan7.OptimizedProfile instance.

• pyhmmer.hmmer.hmmpress emulating the hmmpress binary from HMMER.

• M property to pyhmmer.plan7.HMM exposing the number of nodes in the model.

Changed

• Bumped vendored Easel to v0.48.

• Bumped vendored HMMER to v3.3.2.

• pyhmmer.plan7.HMMFile will raise an EOFError when given an empty file.

• Renamed length property to L in pyhmmer.plan7.Background.

Fixed

• Segmentation fault when close method of pyhmmer.easel.SSIWriter was called more than once.

• close method of pyhmmer.easel.SSIWriter not writing the index contents.

v0.1.0-a4 - 2020-11-24

Added

• MSA, TextMSA and DigitalMSA classes representing a multiple sequence alignment to pyhmmer.easel.

• Methods and protocol to copy a Sequence and a MSA.

• pyhmmer.plan7.OptimizedProfile wrapping a platform-specific optimized profile.

• SSIReader and SSIWriter classes interacting with sequence/subsequence indices to pyhmmer.easel.

• Exception handler using Python exceptions to report Easel errors.

Changed

• pyhmmer.hmmsearch returns an iterator of TopHits, with one instance per HMM in the input.

• pyhmmer.hmmsearch properly raises errors happenning in the background threads without deadlock.

• pyhmmer.plan7.Pipeline recycles memory between Pipeline.search calls.

Fixed

• Missing type annotations for the pyhmmer.errors module.

Removed

• Unneeded or private methods from pyhmmer.plan7.

v0.1.0-a3 - 2020-11-19

Added

• TextSequence and DigitalSequence representing a Sequence in a given mode.

• E-value properties to Hit and Domain.

• TopHits now stores a reference to the pipeline it was obtained from.

• Pipeline.Z and Pipeline.domZ properties.

• Experimental pickling support to Alphabet.

• Experimental freelist to Sequence class to avoid allocation bottlenecks when iterating on a SequenceFile without recycling sequence buffers.

Changed

• Made Sequence an abstract base class.

• Additional Pipeline parameters can be passed as keyword arguments to pyhmmer.hmmsearch.

• SequenceFile.read can now be configured to skip reading the metadata or the content of a sequence.

Removed

• Redundant SequenceFile methods.

Fixed

• doctest loader crashing on Python 3.5.

• TopHits.threshold segfaulting when being called without prior Tophits.sort call

• Unknown format argument to SequenceFile constructor not raising the right error.

v0.1.0-a2 - 2020-11-12

Added

• Support for compilation on PowerPC big-endian platforms.

• Type annotations and stub files for Cython modules.

Changed

• distutils is now used to compile the package, instead of calling autotools and letting HMMER configure itself.

• Bitfield.count now allows passing an argument (for compatibility with collections.abc.Sequence).

v0.1.0-a1 - 2020-11-10

Initial alpha release (test deployment to PyPI).