Fix issue #5 and add ConfigManager

CodonTransformer/CodonData.py

@@ -7,6 +7,7 @@
 
 import json
 import os
+import random
 from typing import Dict, List, Optional, Tuple, Union
 
 import pandas as pd
@@ -25,6 +26,7 @@
     STOP_CODONS,
     STOP_SYMBOL,
     STOP_SYMBOLS,
+    ProteinConfig,
     find_pattern_in_fasta,
     get_taxonomy_id,
     sort_amino2codon_skeleton,
@@ -162,7 +164,7 @@ def preprocess_protein_sequence(protein: str) -> str:
         str: The preprocessed protein sequence.
 
     Raises:
-        ValueError: If the protein sequence is invalid.
+        ValueError: If the protein sequence is invalid or if the configuration is invalid.
     """
     if not protein:
         raise ValueError("Protein sequence is empty.")
@@ -172,10 +174,28 @@ def preprocess_protein_sequence(protein: str) -> str:
         protein.upper().strip().replace("\n", "").replace(" ", "").replace("\t", "")
     )
 
-    # Replace ambiguous amino acids with standard 20 amino acids
-    protein = "".join(
-        AMBIGUOUS_AMINOACID_MAP.get(aminoacid, aminoacid) for aminoacid in protein
-    )
+    # Handle ambiguous amino acids based on the specified behavior
+    config = ProteinConfig()
+    ambiguous_aminoacid_map_override = config.get('ambiguous_aminoacid_map_override')
+    ambiguous_aminoacid_behavior = config.get('ambiguous_aminoacid_behavior')
+    ambiguous_aminoacid_map = AMBIGUOUS_AMINOACID_MAP.copy()
+
+    for aminoacid, standard_aminoacids in ambiguous_aminoacid_map_override.items():
+        ambiguous_aminoacid_map[aminoacid] = standard_aminoacids
+
+    if ambiguous_aminoacid_behavior == 'raise_error':
+        if any(aminoacid in ambiguous_aminoacid_map for aminoacid in protein):
+            raise ValueError("Ambiguous amino acids found in protein sequence.")
+    elif ambiguous_aminoacid_behavior == 'standardize_deterministic':
+        protein = "".join(
+            ambiguous_aminoacid_map.get(aminoacid, [aminoacid])[0] for aminoacid in protein
+        )
+    elif ambiguous_aminoacid_behavior == 'standardize_random':
+        protein = "".join(
+            random.choice(ambiguous_aminoacid_map.get(aminoacid, [aminoacid])) for aminoacid in protein
+        )
+    else:
+        raise ValueError(f"Invalid ambiguous_aminoacid_behavior: {ambiguous_aminoacid_behavior}.")
 
     # Check for sequence validity
     if any(aminoacid not in AMINO_ACIDS + STOP_SYMBOLS for aminoacid in protein):

CodonTransformer/CodonUtils.py

@@ -8,6 +8,7 @@
 import os
 import pickle
 import re
+from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from typing import Any, Dict, Iterator, List, Optional, Tuple
 
@@ -41,13 +42,13 @@
 STOP_SYMBOLS = ["_", "*"]  # Stop codon symbols
 
 # Dictionary ambiguous amino acids to standard amino acids
-AMBIGUOUS_AMINOACID_MAP: Dict[str, str] = {
-    "B": "N",  # Aspartic acid (D) or Asparagine (N)
-    "Z": "Q",  # Glutamic acid (E) or Glutamine (Q)
-    "X": "A",  # Any amino acid (typically replaced with Alanine)
-    "J": "L",  # Leucine (L) or Isoleucine (I)
-    "U": "C",  # Selenocysteine (typically replaced with Cysteine)
-    "O": "K",  # Pyrrolysine (typically replaced with Lysine)
+AMBIGUOUS_AMINOACID_MAP: Dict[str, list[str]] = {
+    "B": ["N", "D"],  # Asparagine (N) or Aspartic acid (D)
+    "Z": ["Q", "E"],  # Glutamine (Q) or Glutamic acid (E)
+    "X": ["A"],  # Any amino acid (typically replaced with Alanine)
+    "J": ["L", "I"],  # Leucine (L) or Isoleucine (I)
+    "U": ["C"],  # Selenocysteine (typically replaced with Cysteine)
+    "O": ["K"],  # Pyrrolysine (typically replaced with Lysine)
 }
 
 # List of all possible start and stop codons
@@ -545,6 +546,132 @@ def __init__(self, data_path: str, train: bool = True, **kwargs):
         self.train = train
 
 
+class ConfigManager(ABC):
+    """
+    Abstract base class for managing configuration settings.
+    """
+    def __init__(self):
+        self._config: Dict[str, Any] = {}
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        if exc_type is not None:
+            print(f"Exception occurred: {exc_type}, {exc_value}, {traceback}")
+        self.reset_config()
+
+    @abstractmethod
+    def reset_config(self) -> None:
+        """Reset the configuration to default values."""
+        pass
+
+    def get(self, key: str) -> Any:
+        """
+        Get the value of a configuration key.
+
+        Args:
+            key (str): The key to retrieve the value for.
+
+        Returns:
+            Any: The value of the configuration key.
+        """
+        return self._config.get(key)
+
+    def set(self, key: str, value: Any) -> None:
+        """
+        Set the value of a configuration key.
+
+        Args:
+            key (str): The key to set the value for.
+            value (Any): The value to set for the key.
+        """
+        self.validate_inputs(key, value)
+        self._config[key] = value
+
+    def update(self, config_dict: dict) -> None:
+        """
+        Update the configuration with a dictionary of key-value pairs after validating them.
+
+        Args:
+            config_dict (dict): A dictionary of key-value pairs to update the configuration.
+        """
+        for key, value in config_dict.items():
+            self.validate_inputs(key, value)
+        self._config.update(config_dict)
+
+    @abstractmethod
+    def validate_inputs(self, key: str, value: Any) -> None:
+        """Validate the inputs for the configuration."""
+        pass
+
+class ProteinConfig(ConfigManager):
+    """
+    A class to manage configuration settings for protein sequences.
+
+    This class ensures that the configuration is a singleton.
+    It provides methods to get, set, and update configuration values.
+
+    Attributes:
+        _instance (Optional[ConfigManager]): The singleton instance of the ConfigManager.
+        _config (Dict[str, Any]): The configuration dictionary.
+    """
+    _instance = None
+
+    def __new__(cls):
+        """
+        Create a new instance of the ProteinConfig class.
+
+        Returns:
+            ProteinConfig: The singleton instance of the ProteinConfig.
+        """
+        if cls._instance is None:
+            cls._instance = super(ProteinConfig, cls).__new__(cls)
+            cls._instance.reset_config()
+        return cls._instance
+
+    def validate_inputs(self, key: str, value: Any) -> None:
+        """
+        Validate the inputs for the configuration.
+
+        Args:
+            key (str): The key to validate.
+            value (Any): The value to validate.
+
+        Raises:
+            ValueError: If the value is invalid.
+            TypeError: If the value is of the wrong type.
+        """
+        if key == 'ambiguous_aminoacid_behavior':
+            if value not in [
+                'raise_error',
+                'standardize_deterministic',
+                'standardize_random'
+            ]:
+                raise ValueError(f"Invalid value for ambiguous_aminoacid_behavior: {value}.")
+        elif key == 'ambiguous_aminoacid_map_override':
+            if not isinstance(value, dict):
+                raise TypeError(f"Invalid type for ambiguous_aminoacid_map_override: {value}.")
+            for ambiguous_aminoacid, aminoacids in value.items():
+                if not isinstance(aminoacids, list):
+                    raise TypeError(f"Invalid type for aminoacids: {aminoacids}.")
+                if not aminoacids:
+                    raise ValueError(f"Override for aminoacid '{ambiguous_aminoacid}' cannot be empty list.")
+                if ambiguous_aminoacid not in AMBIGUOUS_AMINOACID_MAP:
+                    raise ValueError(f"Invalid amino acid in ambiguous_aminoacid_map_override: {ambiguous_aminoacid}")
+        else:
+            raise ValueError(f"Invalid configuration key: {key}")
+
+    def reset_config(self) -> None:
+        """
+        Reset the configuration to the default values.
+        """
+        self._config = {
+            'ambiguous_aminoacid_behavior': 'raise_error',
+            'ambiguous_aminoacid_map_override': {}
+        }
+
+
 def load_python_object_from_disk(file_path: str) -> Any:
     """
     Load a Pickle object from disk and return it as a Python object.

tests/test_CodonData.py

@@ -9,10 +9,32 @@
     get_amino_acid_sequence,
     is_correct_seq,
     read_fasta_file,
+    preprocess_protein_sequence,
 )
-
+from CodonTransformer.CodonUtils import ProteinConfig
 
 class TestCodonData(unittest.TestCase):
+    def test_preprocess_protein_sequence(self):
+        with ProteinConfig() as config:
+            protein = "Z_"
+            try:
+                preprocess_protein_sequence(protein)
+                self.fail("Expected ValueError")
+            except ValueError:
+                pass
+            config.set("ambiguous_aminoacid_behavior", "standardize_deterministic")
+            for _ in range(10):
+                preprocessed_protein = preprocess_protein_sequence(protein)
+                self.assertEqual(preprocessed_protein, "Q_")
+            config.set("ambiguous_aminoacid_behavior", "standardize_random")
+            random_results = set()
+            # The probability of getting the same result 30 times in a row is
+            # 1 in 1.073741824*10^9 if there are only two possible results.
+            for _ in range(30):
+                preprocessed_protein = preprocess_protein_sequence(protein)
+                random_results.add(preprocessed_protein)
+            self.assertGreater(len(random_results), 1)
+
     def test_read_fasta_file(self):
         fasta_content = ">sequence1\n" "ATGATGATGATGATG\n" ">sequence2\n" "TGATGATGATGA"
 

tests/test_CodonUtils.py

@@ -4,6 +4,7 @@
 import unittest
 
 from CodonTransformer.CodonUtils import (
+    ProteinConfig,
     find_pattern_in_fasta,
     get_organism2id_dict,
     get_taxonomy_id,
@@ -15,6 +16,51 @@
 
 
 class TestCodonUtils(unittest.TestCase):
+    def test_config_manager(self):
+        with ProteinConfig() as config:
+            config.set(
+                "ambiguous_aminoacid_behavior",
+                "standardize_deterministic"
+            )
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_behavior"),
+                "standardize_deterministic"
+            )
+            config.set(
+                "ambiguous_aminoacid_map_override",
+                {"R": ["A", "G"]}
+            )
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_map_override"),
+                {"R": ["A", "G"]}
+            )
+            config.update({
+                "ambiguous_aminoacid_behavior": "raise_error",
+                "ambiguous_aminoacid_map_override": {"X": ["A", "G"]},
+            })
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_behavior"),
+                "raise_error"
+            )
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_map_override"),
+                {"X": ["A", "G"]}
+            )
+            try:
+                config.set("invalid_key", "invalid_value")
+                self.fail("Expected ValueError")
+            except ValueError:
+                pass
+        with ProteinConfig() as config:
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_behavior"),
+                "raise_error"
+            )
+            self.assertEqual(
+                config.get("ambiguous_aminoacid_map_override"),
+                {}
+            )
+
     def test_load_python_object_from_disk(self):
         test_obj = {"key1": "value1", "key2": 2}
         with tempfile.NamedTemporaryFile(suffix=".pkl", delete=False) as temp_file: