Create utils.py

code/utils.py

@@ -0,0 +1,70 @@
+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