# sequences

Strategies for generating biological sequences.

# dna()

@composite
def dna(draw, allow_ambiguous=True, allow_gaps=True, uppercase_only=False, min_size=0, max_size: Optional[int] = None)

Generates DNA sequences.

# Arguments

• allow_ambiguous: Whether ambiguous bases are permitted.
• allow_gaps: Whether a - may be in the DNA sequence.
• uppercase_only: Whether to use only uppercase characters.
• min_size: The shortest DNA sequence to generate.
• max_size: The longest DNA sequence to generate.

# rna()

@composite
def rna(draw, allow_ambiguous=True, allow_gaps=True, allow_lowercase=True, min_size=0, max_size: Optional[int] = None)

Generates RNA sequences.

# Arguments

• allow_ambiguous: Whether ambiguous bases are permitted.
• allow_gaps: Whether a - may be in the RNA sequence.
• allow_lowercase: Whether lowercase characters should be used.
• min_size: The shortest RNA sequence to generate
• max_size: The longest RNA sequence to generate

# protein()

@composite
def protein(draw, allow_extended=False, allow_ambiguous=True, single_letter_protein=True, uppercase_only=False, min_size=0, max_size: Optional[int] = None)

Generates protein sequences.

# Arguments

• allow_extended: Whether the extended amino acid alphabet should be used.
• allow_ambiguous: Whether ambiguous amino acids are permitted.
• single_letter_protein: Whether 1-letter or 3-letter abbreviations of proteins should be used.
• uppercase_only: Whether to restrict the protein sequence to uppercase characters.
• min_size: The shortest protein sequence to generate.
• max_size: The longest protein sequence to generate.

# start_codon()

@composite
def start_codon(draw, allow_ambiguous=True) -> str

Generates start codons.

# Arguments

• allow_ambiguous: Whether ambiguous bases are permitted.

# stop_codon()

@composite
def stop_codon(draw, allow_ambiguous=True) -> str

Generates stop codons.

# Arguments

• allow_ambiguous: Whether ambiguous bases are permitted.

# cds()

@composite
def cds(draw, include_start_codon=True, include_stop_codon=True, allow_internal_stop_codons=True, allow_ambiguous=True, uppercase_only=False, min_size=0, max_size=None) -> str

Generates coding DNA sequences (CDSs).

# Arguments

• include_start_codon: Whether to include a start codon at the beginning.
• include_stop_codon: Whether to include a stop codon at the end.
• allow_internal_stop_codons: Whether stop codons may occur at any place other than the end.
• allow_ambiguous: Whether ambiguous bases are permitted.
• uppercase_only: Whether to use only uppercase characters.
• min_size: The shortest CDS to generate in base pairs.
• max_size: The longest CDS to generate in base pairs.

# kmers()

@composite
def kmers(draw, seq: str, k: int) -> str

Generates k-mers (short sliding window substrings) from a given sequence.

# Arguments

• seq: The sequence to be used for generating k-mers
• k: Size of the substrings to be generated