deepfold.data.tools.hmmsearch.Hmmsearch

class deepfold.data.tools.hmmsearch.Hmmsearch(*, binary_path: str, hmmbuild_binary_path: str, database_path: str, flags: Sequence[str] | None = None)

Python wrapper of the hmmsearch binary.

__init__(*, binary_path: str, hmmbuild_binary_path: str, database_path: str, flags: Sequence[str] | None = None)

Initializes the Python hmmsearch wrapper.

Parameters:

• binary_path – The path to the hmmsearch executable.

• hmmbuild_binary_path – The path to the hmmbuild executable. Used to build an hmm from an input a3m.

• database_path – The path to the hmmsearch database (FASTA format).

• flags – List of flags to be used by hmmsearch.

Raises:

RuntimeError – If hmmsearch binary not found within the path.

Methods

__init__(*, binary_path, ...[, flags])	Initializes the Python hmmsearch wrapper.
get_template_hits(output_string, input_sequence)	Gets parsed template hits from the raw string output by the tool.
query(msa_sto[, output_dir])	Queries the database using hmmsearch using a given stockholm msa.
query_with_hmm(hmm[, output_dir])	Queries the database using hmmsearch using a given hmm.

Attributes

input_format
output_format