genetics.dna2aminoacid()

Convert a DNA sequence from a FASTA file to an amino acid sequence.

Usage

Source

genetics.dna2aminoacid(
    fasta_file,
    codons=None,
)

This function reads a FASTA-formatted file, extracts the DNA sequence (skipping the header line that starts with ‘>’), and translates it into an amino acid sequence using the genetic code. The sequence is processed in groups of three nucleotides (codons), and each codon is looked up in the codon dictionary to determine the corresponding amino acid.

Parameters

fasta_file: str

Path to the FASTA file containing the DNA sequence.

codons: dict = None

Dictionary mapping 3-letter DNA codons to single-letter amino acid codes. Defaults to the standard genetic code.

Returns

str: str

The translated amino acid sequence as a single-letter code string.

Raises

FileNotFoundError

If the FASTA file cannot be found.

KeyError

If an invalid codon (not in the dictionary) is encountered.

ValueError

If the DNA sequence length is not a multiple of 3.

Examples

    >>> sequence = dna2aminoacid("sequence.fasta")
    >>> print(sequence)

MKTAYIAKQR...