adding decision tree for HMM inference

barcode_validator/translation_tables.py

@@ -0,0 +1,64 @@
+from enum import Enum
+
+"""
+SYNOPSIS
+    >>> taxonomy = {
+    >>>    'phylum': 'Chordata',
+    >>>    'class': 'Mammalia',
+    >>>    'family': 'Hominidae'
+    >>> }
+    >>> translation_table = get_translation_table(Marker.COI_5P, taxonomy)
+"""
+
+class Marker(Enum):
+    COI_5P = "COI-5P"
+    MATK = "matK"
+    RBCL = "rbcL"
+
+
+def get_translation_table(marker: Marker, taxonomy_dict: dict) -> int:
+    """
+    Determine the appropriate translation table based on marker and taxonomy.
+
+    Args:
+        marker: The genetic marker being analyzed
+        taxonomy_dict: Dictionary containing taxonomic classification with keys:
+            'phylum', 'class', 'family'
+
+    Returns:
+        int: Translation table index for use with Biopython
+    """
+
+    if marker in [Marker.MATK, Marker.RBCL]:
+        if taxonomy_dict.get('family') == 'Balanophoraceae':
+            return 32
+        return 11
+
+    elif marker == Marker.COI_5P:
+        phylum = taxonomy_dict.get('phylum')
+        tax_class = taxonomy_dict.get('class')
+        family = taxonomy_dict.get('family')
+
+        if phylum == 'Chordata':
+            if tax_class == 'Ascidiacea':
+                return 13
+            elif tax_class in ['Actinopteri', 'Amphibia', 'Mammalia', 'Aves', 'Reptilia']:
+                return 2
+
+        elif phylum == 'Hemichordata':
+            if family == 'Cephalodiscidae':
+                return 33
+            elif family == 'Rhabdopleuridae':
+                return 24
+
+        elif phylum in ['Echinodermata', 'Platyhelminthes']:
+            return 9
+
+        # Default invertebrate mitochondrial code for other invertebrates
+        if phylum != 'Chordata':
+            return 5
+
+        # Fall back to standard code if no specific rules match
+        return 1
+
+