Fasta

Functionalities for import and access to protein sequence databases from FASTA files.

This module serves as an interface to the profasta library, offering a convenient way to generate a profasta.db.ProteinDatabase from one or multiple FASTA files. It supports custom FASTA header parsing through a configurable header parser.

Functions:

Name	Description
import_protein_database	Generates a protein database from one or a list of fasta files.

import_protein_database

import_protein_database(
    fasta_path: str | Path | Iterable[str | Path],
    header_parser: str = "uniprot",
) -> ProteinDatabase

Generates a protein database from one or a list of fasta files.

Parameters:

Name	Type	Description	Default
fasta_path	str | Path | Iterable[str | Path]	Path to a fasta file, or a list of paths. The path can be either a string or a pathlib.Path instance.	required
header_parser	str	Allows specifying the name of the parser to use for parsing the FASTA headers. The specified parser must be registered in the global parser registry. By default a strict uniprot parser is used.	'uniprot'

Returns:

Type	Description
ProteinDatabase	A protein database containing entries from the parsed fasta files.

Source code in msreport\fasta.py

def import_protein_database(
    fasta_path: str | pathlib.Path | Iterable[str | pathlib.Path],
    header_parser: str = "uniprot",
) -> ProteinDatabase:
    """Generates a protein database from one or a list of fasta files.

    Args:
        fasta_path: Path to a fasta file, or a list of paths. The path can be either a
            string or a pathlib.Path instance.
        header_parser: Allows specifying the name of the parser to use for parsing the
            FASTA headers. The specified parser must be registered in the global parser
            registry. By default a strict uniprot parser is used.

    Returns:
        A protein database containing entries from the parsed fasta files.
    """
    database = ProteinDatabase()
    paths = [fasta_path] if isinstance(fasta_path, (str, pathlib.Path)) else fasta_path
    for path in paths:
        if isinstance(path, pathlib.Path):
            path = path.as_posix()
        database.add_fasta(path, header_parser=header_parser, overwrite=True)
    return database