debase 0.6.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

debase/lineage_format.py

@@ -30,6 +30,7 @@ from __future__ import annotations
 
 import argparse
 import csv
+import difflib
 import json
 import logging
 import os
@@ -212,8 +213,8 @@ class VariantRecord:
         return result
 
 
-    def ttn_or_yield(self) -> Optional[float]:
-        for col in ("ttn", "yield"):
+    def get_fitness_value(self) -> Optional[float]:
+        for col in ("ttn", "tof", "yield"):
             val = self.row.get(col)
             if val is not None and pd.notna(val):
                 try:
@@ -726,7 +727,49 @@ Only include matches you are confident about. If no match exists, omit that enzy
                             gemini_matched_count += 1
                             log.info(f"Gemini matched '{substrate_id}' -> '{matched_id}' in campaign {campaign_id}")
                         else:
-                            log.warning(f"Gemini suggested match '{matched_id}' not found in sequence lookup")
+                            # Try fuzzy matching when exact match fails
+                            best_match = None
+                            best_score = 0
+                            
+                            # Try all possible keys in seq_lookup
+                            for key in seq_lookup.keys():
+                                if campaign_id in key:  # Only consider keys from same campaign
+                                    # Extract enzyme_id part from composite key
+                                    try:
+                                        _, key_enzyme_id = key.split('_', 1)
+                                    except ValueError:
+                                        continue
+                                    
+                                    # Calculate similarity score
+                                    score = difflib.SequenceMatcher(None, matched_id.lower(), key_enzyme_id.lower()).ratio()
+                                    
+                                    # Always track the highest score
+                                    if score > best_score:
+                                        best_score = score
+                                        best_match = key
+                            
+                            # Use the best match regardless of threshold (let user see the score)
+                            if best_match and best_score > 0.5:  # Lower threshold but log the score
+                                idx = entry["idx"]
+                                df.at[idx, "protein_sequence"] = seq_lookup[best_match]["aa_sequence"]
+                                df.at[idx, "aa_sequence"] = seq_lookup[best_match]["aa_sequence"]
+                                if seq_lookup[best_match]["nt_sequence"]:
+                                    df.at[idx, "nucleotide_sequence"] = seq_lookup[best_match]["nt_sequence"]
+                                    df.at[idx, "nt_sequence"] = seq_lookup[best_match]["nt_sequence"]
+                                
+                                # Also copy generation and parent_enzyme_id
+                                df.at[idx, "generation"] = seq_lookup[best_match]["generation"]
+                                df.at[idx, "parent_enzyme_id"] = seq_lookup[best_match]["parent_enzyme_id"]
+                                
+                                # Store the match for later mutation copying
+                                _, matched_enzyme = best_match.split('_', 1)
+                                df.at[idx, "_matched_enzyme_id"] = matched_enzyme
+                                df.at[idx, "_matched_campaign_id"] = campaign_id
+                                
+                                gemini_matched_count += 1
+                                log.info(f"Fuzzy matched '{substrate_id}' -> '{matched_enzyme}' (score: {best_score:.2f}) in campaign {campaign_id}")
+                            else:
+                                log.warning(f"No fuzzy match found for Gemini suggested '{matched_id}' in campaign {campaign_id} (best score: {best_score:.2f})")
                 
             except Exception as e:
                 log.warning(f"Failed to get Gemini matches for campaign {campaign_id}: {e}")
@@ -1229,9 +1272,15 @@ def flatten_dataframe(df: pd.DataFrame) -> pd.DataFrame:
 
         # Fitness type -------------------------------------------------------
         fitness_type = ""
-        if rec.ttn_or_yield() is not None:
+        if rec.get_fitness_value() is not None:
             ttn_val = row.get("ttn")
-            fitness_type = "ttn" if (ttn_val is not None and pd.notna(ttn_val)) else "yield"
+            tof_val = row.get("tof")
+            if ttn_val is not None and pd.notna(ttn_val):
+                fitness_type = "ttn"
+            elif tof_val is not None and pd.notna(tof_val):
+                fitness_type = "tof"
+            else:
+                fitness_type = "yield"
         
         # Additional info -----------------------------------------------------
         extra: Dict[str, str] = {
@@ -1252,7 +1301,7 @@ def flatten_dataframe(df: pd.DataFrame) -> pd.DataFrame:
             amino_acid_substitutions=aa_muts,
             nt_sequence=rec.nt_seq,
             aa_sequence=rec.aa_seq,
-            fitness_value=rec.ttn_or_yield(),
+            fitness_value=rec.get_fitness_value(),
             fitness_type=fitness_type,
             cofactor=cofactor,
             reaction_condition=reaction_condition,