bioutils.sequences module

Simple functions and lookup tables for nucleic acid and amino acid sequences.

bioutils.sequences.aa1_to_aa3(seq)

Converts string of 1-letter amino acids to 3-letter amino acids.

Should only be used if the format of the sequence is known; otherwise use aa_to_aa3().

Parameters

seq (str) – An amino acid sequence as 1-letter amino acids.

Returns

The sequence as 3-letter amino acids.

Return type

str

Raises

KeyError – If the sequence is not of 1-letter amino acids.

Examples

>>> aa1_to_aa3("CATSARELAME")
'CysAlaThrSerAlaArgGluLeuAlaMetGlu'

>>> aa1_to_aa3(None)

bioutils.sequences.aa3_to_aa1(seq)

Converts string of 3-letter amino acids to 1-letter amino acids.

Should only be used if the format of the sequence is known; otherwise use aa_to_aa1().

Parameters

seq (str) – An amino acid sequence as 3-letter amino acids.

Returns

The sequence as 1-letter amino acids.

Return type

str

Raises

KeyError – If the sequence is not of 3-letter amino acids.

Examples

>>> aa3_to_aa1("CysAlaThrSerAlaArgGluLeuAlaMetGlu")
'CATSARELAME'

>>> aa3_to_aa1(None)

bioutils.sequences.aa_to_aa1(seq)

Coerces string of 1- or 3-letter amino acids to 1-letter representation.

Parameters

seq (str) – An amino acid sequence.

Returns

The sequence as one of 1-letter amino acids.

Return type

str

Examples

>>> aa_to_aa1("CATSARELAME")
'CATSARELAME'

>>> aa_to_aa1("CysAlaThrSerAlaArgGluLeuAlaMetGlu")
'CATSARELAME'

>>> aa_to_aa1(None)

bioutils.sequences.aa_to_aa3(seq)

Coerces string of 1- or 3-letter amino acids to 3-letter representation.

Parameters

seq (str) – An amino acid sequence.

Returns

The sequence as one of 3-letter amino acids.

Return type

str

Examples

>>> aa_to_aa3("CATSARELAME")
'CysAlaThrSerAlaArgGluLeuAlaMetGlu'

>>> aa_to_aa3("CysAlaThrSerAlaArgGluLeuAlaMetGlu")
'CysAlaThrSerAlaArgGluLeuAlaMetGlu'

>>> aa_to_aa3(None)

bioutils.sequences.complement(seq)

Retrieves the complement of a sequence.

Parameters

seq (str) – A nucleotide sequence.

Returns

The complement of the sequence.

Return type

str

Examples

>>> complement("ATCG")
'TAGC'

>>> complement(None)

bioutils.sequences.elide_sequence(s, flank=5, elision='...')

Trims the middle of the sequence, leaving the right and left flanks.

Parameters

• s (str) – A sequence.

• flank (int, optional) – The length of each flank. Defaults to five.

• elision (str, optional) – The symbol used to represent the part trimmed. Defaults to ‘…’.

• Returns – str: The sequence with the middle replaced by elision.

Examples

>>> elide_sequence("ABCDEFGHIJKLMNOPQRSTUVWXYZ")
'ABCDE...VWXYZ'

>>> elide_sequence("ABCDEFGHIJKLMNOPQRSTUVWXYZ", flank=3)
'ABC...XYZ'

>>> elide_sequence("ABCDEFGHIJKLMNOPQRSTUVWXYZ", elision="..")
'ABCDE..VWXYZ'

>>> elide_sequence("ABCDEFGHIJKLMNOPQRSTUVWXYZ", flank=12)
'ABCDEFGHIJKLMNOPQRSTUVWXYZ'

>>> elide_sequence("ABCDEFGHIJKLMNOPQRSTUVWXYZ", flank=12, elision=".")
'ABCDEFGHIJKL.OPQRSTUVWXYZ'

bioutils.sequences.looks_like_aa3_p(seq)

Indicates whether a string looks like a 3-letter AA string.

Parameters

seq (str) – A sequence.

Returns

Whether the string is of the format of a 3-letter AA string.

Return type

bool

bioutils.sequences.normalize_sequence(seq)

Converts sequence to normalized representation for hashing.

Essentially, removes whitespace and asterisks, and uppercases the string.

Parameters

seq (str) – The sequence to be normalized.

Returns

The sequence as a string of uppercase letters.

Return type

str

Raises

RuntimeError – If the sequence contains non-alphabetic characters (besides ‘*’).

Examples

>>> normalize_sequence("ACGT")
'ACGT'

>>> normalize_sequence("  A C G T * ")
'ACGT'

>>> normalize_sequence("ACGT1")
Traceback (most recent call last):
...
RuntimeError: Normalized sequence contains non-alphabetic characters

bioutils.sequences.replace_t_to_u(seq)

Replaces the T’s in a sequence with U’s.

Parameters

seq (str) – A nucleotide sequence.

Returns

The sequence with the T’s replaced by U’s.

Return type

str

Examples

>>> replace_t_to_u("ACGT")
'ACGU'

>>> replace_t_to_u(None)

bioutils.sequences.replace_u_to_t(seq)

Replaces the U’s in a sequence with T’s.

Parameters

seq (str) – A nucleotide sequence.

Returns

The sequence with the U’s replaced by T’s.

Return type

str

Examples

>>> replace_u_to_t("ACGU")
'ACGT'

>>> replace_u_to_t(None)

bioutils.sequences.reverse_complement(seq)

Converts a sequence to its reverse complement.

Parameters

seq (str) – A nucleotide sequence.

Returns

The reverse complement of the sequence.

Return type

str

Examples

>>> reverse_complement("ATCG")
'CGAT'

>>> reverse_complement(None)

bioutils.sequences.translate_cds(seq, full_codons=True, ter_symbol='*')

Translates a DNA or RNA sequence into a single-letter amino acid sequence.

Uses the NCBI standard translation table.

Parameters

• seq (str) – A nucleotide sequence.

• full_codons (bool, optional) – If True, forces sequence to have length that is a multiple of 3 and raises an error otherwise. If False, ter_symbol will be added as the last amino acid. This corresponds to biopython’s behavior of padding the last codon with N``s. Defaults to ``True.

• ter_symbol (str, optional) – Placeholder for the last amino acid if sequence length is not divisible by three and full_codons is False. Defaults to '*'

Returns

The corresponding single letter amino acid sequence.

Return type

str

Raises

• ValueError – If full_codons and the sequence is not a multiple of three.

• ValueError – If a codon is undefined in the table.

Examples

>>> translate_cds("ATGCGA")
'MR'

>>> translate_cds("AUGCGA")
'MR'

>>> translate_cds(None)

>>> translate_cds("")
''

>>> translate_cds("AUGCG")
Traceback (most recent call last):
...
ValueError: Sequence length must be a multiple of three

>>> translate_cds("AUGCG", full_codons=False)
'M*'

>>> translate_cds("ATGTAN")
'MX'

>>> translate_cds("CCN")
'P'

>>> translate_cds("TRA")
'*'

>>> translate_cds("TTNTA", full_codons=False)
'X*'

>>> translate_cds("CTB")
'L'

>>> translate_cds("AGM")
'X'

>>> translate_cds("GAS")
'X'

>>> translate_cds("CUN")
'L'

>>> translate_cds("AUGCGQ")
Traceback (most recent call last):
...
ValueError: Codon CGQ at position 4..6 is undefined in codon table