deepfold.data.tools.hhblits.HHBlits

class deepfold.data.tools.hhblits.HHBlits(*, binary_path: str, databases: Sequence[str], n_cpu: int = 4, n_iter: int = 3, e_value: float = 0.001, maxseq: int = 1000000, realign_max: int = 100000, maxfilt: int = 100000, min_prefilter_hits: int = 1000, all_seqs: bool = False, alt: int | None = None, p: int = 20, z: int = 500)[source]

Python wrapper of the HHblits binary.

__init__(*, binary_path: str, databases: Sequence[str], n_cpu: int = 4, n_iter: int = 3, e_value: float = 0.001, maxseq: int = 1000000, realign_max: int = 100000, maxfilt: int = 100000, min_prefilter_hits: int = 1000, all_seqs: bool = False, alt: int | None = None, p: int = 20, z: int = 500)[source]

Initializes the Python HHblits wrapper.

Parameters:

  • binary_path – The path to the HHblits executable.

  • databases – A sequence of HHblits database paths. This should be the common prefix for the database files (i.e. up to but not including _hhm.ffindex etc.)

  • n_cpu – The number of CPUs to give HHblits.

  • n_iter – The number of HHblits iterations.

  • e_value – The E-value, see HHblits docs for more details.

  • maxseq – The maximum number of rows in an input alignment. Note that this parameter is only supported in HHBlits version 3.1 and higher.

  • realign_max – Max number of HMM-HMM hits to realign. HHblits default: 500.

  • maxfilt – Max number of hits allowed to pass the 2nd prefilter. HHblits default: 20000.

  • min_prefilter_hits – Min number of hits to pass prefilter. HHblits default: 100.

  • all_seqs – Return all sequences in the MSA / Do not filter the result MSA. HHblits default: False.

  • alt – Show up to this many alternative alignments.

  • p – Minimum Prob for a hit to be included in the output hhr file. HHblits default: 20.

  • z – Hard cap on number of hits reported in the hhr file. HHblits default: 500. NB: The relevant HHblits flag is -Z not -z.

Raises:

RuntimeError – If HHblits binary not found within the path.

Methods

__init__(*, binary_path, databases[, n_cpu, ...])

Initializes the Python HHblits wrapper.

query(input_fasta_path)

Queries the database using HHblits.