openfold.data.tools.jackhmmer

Library to run Jackhmmer from Python.

Classes

Jackhmmer(*, binary_path, database_path[, ...])

Python wrapper of the Jackhmmer binary.

class Jackhmmer(*, binary_path, database_path, n_cpu=8, n_iter=1, e_value=0.0001, z_value=None, get_tblout=False, filter_f1=0.0005, filter_f2=5e-05, filter_f3=5e-07, incdom_e=None, dom_e=None, num_streamed_chunks=None, streaming_callback=None)

Python wrapper of the Jackhmmer binary.

Parameters:

• binary_path (str)

• database_path (str)

• n_cpu (int)

• n_iter (int)

• e_value (float)

• z_value (int | None)

• get_tblout (bool)

• filter_f1 (float)

• filter_f2 (float)

• filter_f3 (float)

• incdom_e (float | None)

• dom_e (float | None)

• num_streamed_chunks (int | None)

• streaming_callback (Callable[[int], None] | None)

query(input_fasta_path, max_sequences=None)

Parameters:

• input_fasta_path (str)

• max_sequences (int | None)

Return type:

Sequence[Sequence[Mapping[str, Any]]]

query_multiple(input_fasta_paths, max_sequences=None)

Queries the database using Jackhmmer.

Parameters:

• input_fasta_paths (Sequence[str])

• max_sequences (int | None)

Return type:

Sequence[Sequence[Mapping[str, Any]]]