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def threeToOne(variant):
if variant == "ALA":
variant = "A"
elif variant == "ARG":
variant = "R"
elif variant == "VAL":
variant = "V"
elif variant == "GLU":
variant = "E"
elif variant == "PRO":
variant = "P"
elif variant == "LEU":
variant = "L"
elif variant == "GLY":
variant = "G"
elif variant == "ASN":
variant = "N"
elif variant == "SER":
variant = "S"
elif variant == "GLN":
variant = "Q"
elif variant == "THR":
variant = "T"
elif variant == "MET":
variant = "M"
elif variant == "LYS":
variant = "K"
elif variant == "ASP":
variant = "D"
elif variant == "ILE":
variant = "I"
elif variant == "PHE":
variant = "F"
elif variant == "TRP":
variant = "W"
elif variant == "TYR":
variant = "Y"
elif variant == "HIS":
variant = "H"
elif variant == "CYS":
variant = "C"
elif variant == 'UNK':
variant = 'X'
elif variant == 'ASX':
variant = 'O'
return (variant)
def convert_non_standard_amino_acids(sequence):
"""
Convert non-standard or ambiguous amino acid codes to their closest relatives.
"""
# Define a dictionary to map non-standard codes to standard amino acids
conversion_dict = {
'B': 'D', # Aspartic Acid (D) is often used for B (Asx)
'Z': 'E', # Glutamic Acid (E) is often used for Z (Glx)
'X': 'A', # Alanine (A) is a common placeholder for unknown/ambiguous
'U': 'C', # Cysteine (C) is often used for Selenocysteine (U)
'J': 'L', # Leucine (L) is often used for J (Leu/Ile)
'O': 'K', # Lysine (K) is often used for O (Pyrrolysine)
# '*' or 'Stop' represents a stop codon; you may replace with '' to remove
'*': '',
}
# Replace non-standard codes with their closest relatives
converted_sequence = ''.join([conversion_dict.get(aa, aa) for aa in sequence])
return converted_sequence |