API Reference¶

Cython bindings and Python interface to HMMER3.

HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is maintained by members of the the Eddy/Rivas Laboratory at Harvard University.

pyhmmer is a module, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the HMMER internals, which has several advantages over CLI wrappers like hmmer-py.

HMMER¶

`pyhmmer.hmmer.hmmsearch`	Search HMM profiles against a sequence database.
`pyhmmer.hmmer.phmmer`	Search protein sequences against a sequence database.
`pyhmmer.hmmer.nhmmer`	Search nucleotide sequences against a sequence database.
`pyhmmer.hmmer.hmmpress`	Press several HMMs into a database.
`pyhmmer.hmmer.hmmalign`	Align several sequences to a reference HMM, and return the MSA.

Easel¶

Data Structures¶

`pyhmmer.easel.Bitfield`	A statically sized sequence of booleans stored as a packed bitfield.
`pyhmmer.easel.KeyHash`	A dynamically resized container to store byte keys using a hash table.

Sequences¶

`pyhmmer.easel.Sequence`	An abstract biological sequence with some associated metadata.
`pyhmmer.easel.TextSequence`	A biological sequence stored in text mode.
`pyhmmer.easel.DigitalSequence`	A biological sequence stored in digital mode.
`pyhmmer.easel.SequenceFile`	A wrapper around a sequence file, containing unaligned sequences.

Alignments¶

`pyhmmer.easel.MSA`	An abstract alignment of multiple sequences.
`pyhmmer.easel.TextMSA`	A multiple sequence alignement stored in text mode.
`pyhmmer.easel.DigitalMSA`	A multiple sequence alignment stored in digital mode.
`pyhmmer.easel.MSAFile`	A wrapper around a multiple-alignment file.

Linear Algebra¶

`pyhmmer.easel.Vector`	An abstract 1D array of fixed size.
`pyhmmer.easel.VectorF`	A vector storing single-precision floating point numbers.
`pyhmmer.easel.VectorU8`	A vector storing byte-sized unsigned integers.
`pyhmmer.easel.Matrix`	An abstract 2D array of fixed size.
`pyhmmer.easel.MatrixF`	A matrix storing single-precision floating point numbers.
`pyhmmer.easel.MatrixU8`	A matrix storing byte-sized unsigned integers.

Miscellaneous¶

`pyhmmer.easel.Alphabet`	A biological alphabet, including additional marker symbols.
`pyhmmer.easel.Randomness`	A portable, thread-safe random number generator.
`pyhmmer.easel.SSIReader`	A read-only handler for sequence/subsequence index file.
`pyhmmer.easel.SSIWriter`	A writer for sequence/subsequence index files.

Plan7¶

Hidden Markov Model¶

`pyhmmer.plan7.HMM`	A data structure storing the Plan7 Hidden Markov Model.
`pyhmmer.plan7.HMMFile`	A wrapper around a file (or database), storing serialized HMMs.

Profile¶

`pyhmmer.plan7.Profile`	A Plan7 search profile.
`pyhmmer.plan7.OptimizedProfile`	An optimized profile that uses platform-specific instructions.
`pyhmmer.plan7.Background`	The null background model of HMMER.

Pipelines¶

`pyhmmer.plan7.Pipeline`	An HMMER3 accelerated sequence/profile comparison pipeline.
`pyhmmer.plan7.Builder`	A factory for constructing new HMMs from raw sequences.

Results¶

`pyhmmer.plan7.TopHits`	A ranked list of top-scoring hits.
`pyhmmer.plan7.Hit`	A high-scoring database hit found by the comparison pipeline.
`pyhmmer.plan7.Domains`	A read-only view over the domains of a single `Hit`.
`pyhmmer.plan7.Domain`	A single domain in a query `Hit`.
`pyhmmer.plan7.Alignment`	An alignment of a sequence to a profile.

Traces¶

`pyhmmer.plan7.TraceAligner`	A factory for aligning several sequences to a reference model.
`pyhmmer.plan7.Traces`	A list of tracebacks obtained by aligning several sequences to a model.
`pyhmmer.plan7.Trace`	A traceback for the alignment of a model to a sequence.

Miscellaneous¶

`pyhmmer.plan7.Cutoffs`	A read-only view over the Pfam score cutoffs of a `HMM` or a `Profile`.
`pyhmmer.plan7.EvalueParameters`	A mutable view over the e-value parameters of a `HMM` or a `Profile`.
`pyhmmer.plan7.Offsets`	A mutable view over the disk offsets of a profile.

Errors¶

`pyhmmer.errors.AllocationError`	A memory error that is caused by an unsuccessful allocation.
`pyhmmer.errors.UnexpectedError`	An unexpected error that happened in the C code.
`pyhmmer.errors.EaselError`	An error that was raised from the Easel code.