API Reference ============== .. toctree:: :hidden: hmmer easel plan7 daemon errors .. currentmodule:: pyhmmer .. automodule:: pyhmmer .. only:: html HMMER ----- .. autosummary:: :nosignatures: pyhmmer.hmmer.hmmsearch pyhmmer.hmmer.hmmscan pyhmmer.hmmer.phmmer pyhmmer.hmmer.nhmmer pyhmmer.hmmer.hmmpress pyhmmer.hmmer.hmmalign Easel ----- Data Structures ^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.Bitfield pyhmmer.easel.KeyHash Sequences ^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.Sequence pyhmmer.easel.TextSequence pyhmmer.easel.DigitalSequence Sequence Blocks ^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.SequenceBlock pyhmmer.easel.TextSequenceBlock pyhmmer.easel.DigitalSequenceBlock Sequence File ^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.SequenceFile Alignments ^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.MSA pyhmmer.easel.TextMSA pyhmmer.easel.DigitalMSA Alignment File ^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.MSAFile Linear Algebra ^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.Vector pyhmmer.easel.VectorF pyhmmer.easel.VectorU8 pyhmmer.easel.Matrix pyhmmer.easel.MatrixF pyhmmer.easel.MatrixU8 Miscellaneous ^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.easel.Alphabet pyhmmer.easel.Randomness pyhmmer.easel.SSIReader pyhmmer.easel.SSIWriter Plan7 ----- Profile HMMs ^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.HMM pyhmmer.plan7.Profile pyhmmer.plan7.OptimizedProfile pyhmmer.plan7.OptimizedProfileBlock HMM Files ^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.HMMFile pyhmmer.plan7.HMMPressedFile Pipelines ^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.Pipeline pyhmmer.plan7.LongTargetsPipeline pyhmmer.plan7.Builder pyhmmer.plan7.Background Results ^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.TopHits pyhmmer.plan7.Hit pyhmmer.plan7.Domains pyhmmer.plan7.Domain pyhmmer.plan7.Alignment Traces ^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.TraceAligner pyhmmer.plan7.Traces pyhmmer.plan7.Trace Iterative Searches ^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.IterativeSearch pyhmmer.plan7.IterationResult Miscellaneous ^^^^^^^^^^^^^ .. autosummary:: :nosignatures: pyhmmer.plan7.Cutoffs pyhmmer.plan7.EvalueParameters pyhmmer.plan7.Offsets pyhmmer.plan7.Transitions Daemon ------ .. autosummary:: :nosignatures: pyhmmer.daemon.Client pyhmmer.daemon.IterativeSearch Errors ------ .. autosummary:: :nosignatures: pyhmmer.errors.AllocationError pyhmmer.errors.UnexpectedError pyhmmer.errors.EaselError pyhmmer.errors.AlphabetMismatch pyhmmer.errors.ServerError pyhmmer.errors.MissingCutoffs pyhmmer.errors.InvalidParameter pyhmmer.errors.InvalidHMM