pyhiv.loading package

Submodules

pyhiv.loading.read_fastas module

pyhiv.loading.read_fastas.read_input_fastas(input_folder)

Reads nucleotide FASTA files (.fasta, .fa, .fna, .ffn) from a specified input folder.

Parameters:

input_folder (Path) – Path to the folder containing the FASTA files.

Returns:

A list of BioPython SeqRecord objects containing sequence IDs and sequences.

Return type:

List[SeqRecord]

Raises:

NotADirectoryError – If the input folder does not exist or is not a directory.

Module contents

pyhiv.loading.read_input_fastas(input_folder)

Reads nucleotide FASTA files (.fasta, .fa, .fna, .ffn) from a specified input folder.

Parameters:

input_folder (Path) – Path to the folder containing the FASTA files.

Returns:

A list of BioPython SeqRecord objects containing sequence IDs and sequences.

Return type:

List[SeqRecord]

Raises:

NotADirectoryError – If the input folder does not exist or is not a directory.

pyhiv.loading.validate_reference_paths(paths=None)

Ensure all required reference files and directories exist.

Parameters:

paths (dict[str, Path] | None)