pyhiv.align package

Submodules

pyhiv.align.align_with_reference.align_with_references(test_sequence, references_dir=None, n_jobs=None)[source]

Aligns a test sequence with reference sequences in parallel and returns the best match.

Parameters:

test_sequence (SeqRecord) – A BioPython SeqRecord object representing the test sequence.
references_dir (Path, optional) – Path to the directory containing reference sequences. Defaults to REFERENCE_GENOMES_FASTAS_DIR, containing reference genomes for HIV-1 subtyping.
n_jobs (int, optional) – Number of worker processes to use for parallel processing. Defaults to using all available CPU cores.

Returns:

A tuple containing the test sequence, reference sequence, and the reference file name with the best alignment.

Return type:

Tuple[str, str, str]

pyhiv.align.align_with_reference.calculate_alignment_score(seq1, seq2)[source]

Calculate the alignment score between two sequences.

Parameters:

Returns:

Number of positions where the sequences are equal.

Return type:

int

pyhiv.align.align_with_reference.process_alignment(test_seq, ref_seq)[source]

Aligns test sequence with a reference sequence and calculates the score.

Parameters:

test_seq (SeqRecord) – A BioPython SeqRecord object representing the test sequence.
ref_seq (SeqRecord) – A BioPython SeqRecord object representing the reference sequence.

Returns:

A tuple containing the alignment score, the aligned test sequence, the aligned reference sequence, and the reference sequence name.

Return type:

Tuple[int, str, str, str]

pyhiv.align.famsa.pyfamsa_align(test_seq, ref_seq)[source]

Aligns a test sequence to a reference sequence using the pyfamsa library.

Parameters:

test_seq (SeqRecord) – The test sequence to align. Should be a Biopython SeqRecord object containing the test sequence ID and sequence.
ref_seq (SeqRecord) – The reference sequence to align against. Should be a Biopython SeqRecord object containing the reference sequence ID and sequence.

Returns:

Return type:

tuple