smftools.informatics.sequence_encoding

smftools.informatics.sequence_encoding#

Functions

decode_int_sequence(encoded_sequence, *[, ...])

Decode integer-encoded bases into characters using constant mappings.

encode_sequence_to_int(sequence, *[, ...])

Encode a base sequence into integer values using constant mappings.

phred_to_fastq_quality_string(quality_scores)

Encode integer Phred quality scores as a FASTQ Phred+33 quality string.
smftools.informatics.sequence_encoding.encode_sequence_to_int(sequence, *, base_to_int=mappingproxy({'A': 0, 'C': 1, 'G': 2, 'T': 3, 'N': 4, 'PAD': 5}), unknown_base='N')#

Encode a base sequence into integer values using constant mappings.

Parameters:

  • sequence (Union[str, Iterable[str]]) -- Sequence string or iterable of base characters.

  • base_to_int (Mapping[str, int] (default: mappingproxy({'A': 0, 'C': 1, 'G': 2, 'T': 3, 'N': 4, 'PAD': 5}))) -- Mapping of base characters to integer encodings.

  • unknown_base (str (default: 'N')) -- Base to use when a character is not in the encoding map.

Returns:

Integer-encoded sequence array.

Return type:

np.ndarray

Raises:

ValueError -- If an unknown base is encountered and unknown_base is not mapped.

smftools.informatics.sequence_encoding.decode_int_sequence(encoded_sequence, *, int_to_base=mappingproxy({0: 'A', 1: 'C', 2: 'G', 3: 'T', 4: 'N', 5: 'PAD'}), unknown_base='N')#

Decode integer-encoded bases into characters using constant mappings.

Parameters:

  • encoded_sequence (Union[Iterable[int], ndarray]) -- Iterable of integer-encoded bases.

  • int_to_base (Mapping[int, str] (default: mappingproxy({0: 'A', 1: 'C', 2: 'G', 3: 'T', 4: 'N', 5: 'PAD'}))) -- Mapping of integer encodings to base characters.

  • unknown_base (str (default: 'N')) -- Base to use when an integer is not in the decoding map.

Returns:

Decoded base characters.

Return type:

list[str]

Raises:

ValueError -- If unknown_base is not available for fallback.

smftools.informatics.sequence_encoding.phred_to_fastq_quality_string(quality_scores)#

Encode integer Phred quality scores as a FASTQ Phred+33 quality string.

Values are clamped to [0, 93], the printable-ASCII range for Phred+33 encoding. This also maps the ragged store's -1 missing-quality sentinel (see ragged_store.alignment_to_ragged_record) to Phred 0 ("!").

Parameters:

quality_scores (Iterable[int]) -- Iterable of per-base integer Phred quality scores.

Returns:

FASTQ quality line, one ASCII character per base.

Return type:

str