debase 0.4.4__py3-none-any.whl → 0.5.0__py3-none-any.whl

debase/enzyme_lineage_extractor.py

@@ -24,6 +24,7 @@ import pandas as pd
 import networkx as nx  # light dependency, used only for generation inference
 
 import os
+import fitz
 import re
 import json
 import time
@@ -460,8 +461,32 @@ def get_model():
     if not api_key:
         raise EnvironmentError("Set the GEMINI_API_KEY environment variable.")
     _genai.configure(api_key=api_key)
-    # Positional constructor arg works for both SDK flavors
-    return _genai.GenerativeModel(MODEL_NAME)
+    
+    # Create generation config to optimize performance and costs
+    generation_config = {
+        "temperature": 0.0,  # Deterministic: always pick the most likely token
+        "top_p": 1.0,      # Consider all tokens (but temperature=0 will pick the best)
+        "top_k": 1,        # Only consider the single most likely token
+        "max_output_tokens": 32768,  # Increased from 8192 to handle larger sequence extractions
+    }
+    
+    # For Gemini 2.5 Flash, disable thinking tokens to save costs
+    # thinking_budget=0 disables thinking, -1 enables dynamic thinking (default)
+    # Only add if SDK supports it to maintain compatibility
+    try:
+        # Test if thinking_budget is supported by making a minimal API call
+        test_config = {"thinking_budget": 0, "max_output_tokens": 10}
+        test_model = _genai.GenerativeModel(MODEL_NAME, generation_config=test_config)
+        # Actually test the API call to see if thinking_budget is supported
+        test_response = test_model.generate_content("Return 'OK'")
+        # If no error, add thinking_budget to main config
+        generation_config["thinking_budget"] = 0
+        log.debug("Disabled thinking tokens (thinking_budget=0)")
+    except Exception as e:
+        # SDK doesn't support thinking_budget, continue without it
+        log.debug(f"thinking_budget not supported: {e}")
+    
+    return _genai.GenerativeModel(MODEL_NAME, generation_config=generation_config)
 
 # === 5.3  Unified call helper ----------------------------------------------
 
@@ -728,22 +753,24 @@ Return a JSON object with:
 _LINEAGE_LOC_PROMPT = """
 You are an expert reader of protein engineering manuscripts.
 {campaign_context}
-Given the following article text, list up to {max_results} *locations* (page
-numbers, figure/table IDs, or section headings) that you would review first to
-find the COMPLETE evolutionary lineage of enzyme variants (i.e. which variant
-came from which parent and what mutations were introduced){campaign_specific}.
+Given the following article text, list up to {max_results} *locations* (figure/table IDs
+or section headings) that you would review first to find the COMPLETE evolutionary 
+lineage of enzyme variants (i.e. which variant came from which parent and what 
+mutations were introduced){campaign_specific}. Pay attention to the provided context after the caption
+ensure the location you return are actually lineage location with variants and mutations.
 
 Respond with a JSON array of objects, each containing:
-- "location": the identifier (e.g. "Table S1", "Figure 2B", "6" for page 6, "S6" for supplementary page 6)
-- "type": one of "table", "figure", "text", "section"  
+- "location": the figure/table identifier (e.g. "Table S1", "Figure 2B", "Table 1", "Figure 3")
+- "type": one of "table", "figure", "section"  
 - "confidence": your confidence score (0-100) that this location contains lineage data
 - "reason": brief explanation of why this location likely contains lineage
 {campaign_field}
-IMPORTANT: For page numbers, use ONLY the number (e.g., "6" not "p. 6" or "page 6")
+IMPORTANT: Return ONLY figure/table identifiers like "Figure 2" or "Table S1", 
+NOT page numbers. Focus on the actual figure/table titles and numbers.
 
 Order by confidence score (highest first). Tables showing complete variant lineages or 
-mutation lists should be ranked higher than figure showing complete variant lineages.
-Text sections is used when no suitable tables/figurews exist.
+mutation lists should be ranked higher than figures showing complete variant lineages.
+Sections are used when no suitable tables/figures exist.
 
 Don't include oligonucleotide results or result from only one round.
 
@@ -1713,7 +1740,6 @@ def get_lineage(
         for pdf_path in pdf_paths:
             # Extract first few pages looking for TOC
             try:
-                import fitz  # PyMuPDF
                 doc = fitz.open(pdf_path)
                 toc_text = ""
                 for page_num in range(min(5, doc.page_count)):  # First 5 pages
@@ -2011,7 +2037,7 @@ def identify_sequence_locations(text: str, model, *, debug_dir: str | Path | Non
 
 # --- 7.2  Page-based extraction helper ---------------------------------------
 def _extract_plain_sequence_with_triple_validation(prompt: str, model, context: str = "") -> Optional[str]:
-    """Extract plain text sequence using Gemini with adaptive validation (up to 5 attempts).
+    """Extract plain text sequence using Gemini with 6 attempts, returning most common result.
     
     Args:
         prompt: The prompt to send to Gemini
@@ -2019,12 +2045,12 @@ def _extract_plain_sequence_with_triple_validation(prompt: str, model, context:
         context: Additional context for logging (e.g., "validation" or "extraction")
     
     Returns:
-        The validated sequence or None if no consensus
+        The most common sequence or None if all attempts failed
     """
     sequences = []
-    max_attempts = 5  # Increased from 3 to 5
+    max_attempts = 6
     
-    # Try up to 5 times
+    # Try 6 times
     for attempt in range(max_attempts):
         try:
             response = model.generate_content(prompt)
@@ -2050,38 +2076,14 @@ def _extract_plain_sequence_with_triple_validation(prompt: str, model, context:
         except Exception as e:
             log.warning(f"Gemini {context} attempt {attempt + 1} failed: {e}")
             sequences.append("ERROR")
-        
-        # Check for early consensus after 2 attempts
-        if len(sequences) == 2:
-            # Clean sequences before comparison
-            seq0_clean = sequences[0].replace(" ", "").replace("\n", "") if sequences[0] not in ["INVALID", "ERROR", "VALID", "UNCERTAIN"] else sequences[0]
-            seq1_clean = sequences[1].replace(" ", "").replace("\n", "") if sequences[1] not in ["INVALID", "ERROR", "VALID", "UNCERTAIN"] else sequences[1]
-            
-            if seq0_clean == seq1_clean and sequences[0] not in ["INVALID", "ERROR"]:
-                log.info(f"Gemini {context} consensus reached after 2 attempts")
-                return seq0_clean if seq0_clean not in ["VALID", "UNCERTAIN"] else None
-            else:
-                log.info(f"Gemini {context} mismatch after 2 attempts: {seq0_clean[:20]}... vs {seq1_clean[:20]}... - trying third")
     
-    # After all attempts, find consensus
+    # After all attempts, find most common result
     valid_sequences = [s for s in sequences if s not in ["INVALID", "ERROR"]]
     
     if not valid_sequences:
         log.error(f"All {max_attempts} {context} attempts failed")
         return None
     
-    # Find any matching pair
-    for i in range(len(sequences)):
-        for j in range(i + 1, len(sequences)):
-            # Clean sequences before comparison
-            seq_i_clean = sequences[i].replace(" ", "").replace("\n", "") if sequences[i] not in ["INVALID", "ERROR", "VALID", "UNCERTAIN"] else sequences[i]
-            seq_j_clean = sequences[j].replace(" ", "").replace("\n", "") if sequences[j] not in ["INVALID", "ERROR", "VALID", "UNCERTAIN"] else sequences[j]
-            
-            if seq_i_clean == seq_j_clean and sequences[i] not in ["INVALID", "ERROR"]:
-                log.info(f"Gemini {context} consensus found: attempts {i+1} and {j+1} match")
-                return seq_i_clean if seq_i_clean not in ["VALID", "UNCERTAIN"] else None
-    
-    # If no exact match, use adaptive validation
     # Count occurrences of each valid sequence
     sequence_counts = {}
     for seq in valid_sequences:
@@ -2090,80 +2092,16 @@ def _extract_plain_sequence_with_triple_validation(prompt: str, model, context:
             seq_clean = seq.replace(" ", "").replace("\n", "")
             sequence_counts[seq_clean] = sequence_counts.get(seq_clean, 0) + 1
     
-    # Return the most common sequence if it appears at least twice
+    # Return the most common sequence
     if sequence_counts:
         most_common = max(sequence_counts.items(), key=lambda x: x[1])
-        if most_common[1] >= 2:
-            log.info(f"Gemini {context} adaptive consensus: sequence appeared {most_common[1]}/{len(sequences)} times")
-            return most_common[0]
+        log.info(f"Gemini {context} most common: sequence appeared {most_common[1]}/{max_attempts} times")
+        return most_common[0]
     
-    log.warning(f"Gemini {context} no consensus after {max_attempts} attempts")
+    log.warning(f"Gemini {context} no valid sequences after {max_attempts} attempts")
     return None
 
 
-def _validate_sequence_against_mutations(sequence: str, variants: List[Variant], lineage_text: str, model) -> Optional[str]:
-    """Validate and potentially correct a sequence using Gemini by checking against known mutations."""
-    
-    # Extract mutations from variants
-    mutations = []
-    for variant in variants:
-        if variant.mutations:
-            mutations.extend(variant.mutations)
-    
-    if not mutations:
-        return None
-    
-    # Take a sample of mutations for validation
-    sample_mutations = mutations[:10]  # Check first 10 mutations
-    
-    # First do a quick local check for obvious inconsistencies
-    local_issues = []
-    for mutation in sample_mutations:
-        if hasattr(mutation, 'original') and hasattr(mutation, 'position'):
-            pos = mutation.position - 1  # Convert to 0-indexed
-            if 0 <= pos < len(sequence):
-                actual_aa = sequence[pos]
-                expected_aa = mutation.original
-                if actual_aa != expected_aa:
-                    local_issues.append(f"Position {mutation.position}: expected {expected_aa}, found {actual_aa}")
-    
-    if not local_issues:
-        return None  # No obvious issues found
-    
-    log.info(f"Found {len(local_issues)} potential sequence issues, asking Gemini for validation with triple-check")
-    
-    prompt = f"""
-You are validating a protein sequence that was extracted from a scientific paper.
-The sequence may have OCR errors like duplicated letters (e.g., "II" becoming "III").
-
-Original sequence (length {len(sequence)}):
-{sequence}
-
-Known mutations that should be applicable to this sequence:
-{', '.join(str(m) for m in sample_mutations)}
-
-Potential issues detected:
-{chr(10).join(local_issues)}
-
-Please check if the sequence is consistent with these mutations:
-1. For each mutation (e.g., M263T), check if position 263 (1-indexed) actually has M
-2. If you find inconsistencies, suggest the most likely correction
-3. Common errors include: duplicated letters, missing letters, OCR confusion (like II vs III)
-4. Pay special attention to consecutive identical amino acids that might be OCR errors
-
-Return ONLY the corrected sequence if changes are needed, or "VALID" if no changes are needed.
-If you cannot determine the correct sequence, return "UNCERTAIN".
-"""
-    
-    # Use triple validation
-    result = _extract_plain_sequence_with_triple_validation(prompt, model, "validation")
-    
-    if result == "VALID" or result is None:
-        return None  # No changes needed
-    else:
-        log.info(f"Gemini suggested sequence correction (length {len(result)})")
-        return result
-
 
 def _extract_text_from_page(pdf_paths: List[Path], page_num: Union[str, int], skip_si_toc: bool = True) -> str:
     """Extract text from a specific page number in the PDFs.
@@ -2331,11 +2269,11 @@ CRITICAL: Use the EXACT variant identifier as it appears with each sequence:
 
 SEQUENCE EXTRACTION RULES:
 - Copy sequences EXACTLY as they appear in the text
-- Pay careful attention to repeated amino acids (e.g., "AAA" should remain "AAA", not become "A")
-- Do NOT add, remove, or modify any amino acids
+- Pay careful attention to repeated amino acids, and nucleotides (e.g., "AAA" should remain "AAA", not become "A")
+- Do NOT add, remove, or modify any amino acids, or nucleotides
 - Preserve the exact length and character sequence
 - If a sequence has line breaks or spacing, remove only formatting (spaces, newlines) but keep all amino acids
-- Double-check that consecutive identical amino acids are copied correctly
+- Double-check that consecutive identical amino acids or nucleotides  are copied correctly
 
 For each variant return:
   * variant_id  - the EXACT label as it appears with the sequence (preserve all formatting)
@@ -2356,8 +2294,81 @@ TEXT (may be truncated):
 ```
 """.strip()
 
+def _check_sequence_responses_match(resp1: Union[list, dict], resp2: Union[list, dict]) -> bool:
+    """
+    Check if two sequence extraction responses match.
+    
+    Args:
+        resp1: First response (list of sequences or dict)
+        resp2: Second response (list of sequences or dict)
+        
+    Returns:
+        True if responses match, False otherwise
+    """
+    # Handle None cases
+    if resp1 is None or resp2 is None:
+        return False
+    
+    # Both should be the same type
+    if type(resp1) != type(resp2):
+        return False
+    
+    # If both are lists
+    if isinstance(resp1, list) and isinstance(resp2, list):
+        # Must have same length
+        if len(resp1) != len(resp2):
+            return False
+        
+        # Create normalized sequence sets for comparison
+        seq_set1 = set()
+        seq_set2 = set()
+        
+        for seq in resp1:
+            if isinstance(seq, dict):
+                variant_id = seq.get("variant_id", "")
+                aa_seq = seq.get("aa_seq")
+                dna_seq = seq.get("dna_seq")
+                # Handle None/null values - convert to empty string for comparison
+                if aa_seq is None:
+                    aa_seq = ""
+                else:
+                    aa_seq = aa_seq.replace(" ", "").replace("\n", "").upper()
+                if dna_seq is None:
+                    dna_seq = ""
+                else:
+                    dna_seq = dna_seq.replace(" ", "").replace("\n", "").upper()
+                seq_set1.add(f"{variant_id}|{aa_seq}|{dna_seq}")
+        
+        for seq in resp2:
+            if isinstance(seq, dict):
+                variant_id = seq.get("variant_id", "")
+                aa_seq = seq.get("aa_seq")
+                dna_seq = seq.get("dna_seq")
+                # Handle None/null values - convert to empty string for comparison
+                if aa_seq is None:
+                    aa_seq = ""
+                else:
+                    aa_seq = aa_seq.replace(" ", "").replace("\n", "").upper()
+                if dna_seq is None:
+                    dna_seq = ""
+                else:
+                    dna_seq = dna_seq.replace(" ", "").replace("\n", "").upper()
+                seq_set2.add(f"{variant_id}|{aa_seq}|{dna_seq}")
+        
+        return seq_set1 == seq_set2
+    
+    # If both are dicts, compare normalized content
+    if isinstance(resp1, dict) and isinstance(resp2, dict):
+        # Normalize and compare
+        return json.dumps(resp1, sort_keys=True) == json.dumps(resp2, sort_keys=True)
+    
+    return False
+
+
 def _extract_sequences_with_triple_validation(model, prompt: str, schema_hint: str, *, debug_dir: str | Path | None = None) -> Optional[Any]:
-    """Extract sequence JSON using Gemini with adaptive validation (up to 5 attempts).
+    """Extract sequence JSON using Gemini with up to 6 attempts, returning most common result.
+    
+    Can exit early after 2 attempts if the responses match exactly.
     
     Args:
         model: The Gemini model instance
@@ -2366,12 +2377,12 @@ def _extract_sequences_with_triple_validation(model, prompt: str, schema_hint: s
         debug_dir: Optional debug directory
     
     Returns:
-        The validated sequence JSON data or None if no consensus
+        The most common sequence JSON data or None if all attempts failed
     """
     responses = []
-    max_attempts = 5  # Increased from 3 to 5
+    max_attempts = 6
     
-    # Try up to 5 times
+    # Try 6 times with early match detection
     for attempt in range(max_attempts):
         try:
             log.info(f"Sequence extraction attempt {attempt + 1}/{max_attempts}")
@@ -2443,167 +2454,69 @@ def _extract_sequences_with_triple_validation(model, prompt: str, schema_hint: s
                     else:
                         raise json.JSONDecodeError("No JSON structure found in response", raw, 0)
             
-            # Store both the original and normalized response
-            normalized_response = _normalize_sequence_response(parsed)
-            responses.append((parsed, normalized_response))
-            
-            log.info(f"Sequence extraction attempt {attempt + 1}: {len(normalized_response) if isinstance(normalized_response, list) else 'invalid'} sequences")
+            # Store the response
+            responses.append(parsed)
+            log.info(f"Sequence extraction attempt {attempt + 1}: {len(parsed) if isinstance(parsed, list) else 'object'} sequences")
+            
+            # Early match detection after 2 attempts
+            if attempt >= 1:  # After 2nd attempt (0-indexed)
+                valid_responses_so_far = [r for r in responses if r is not None]
+                if len(valid_responses_so_far) >= 2:
+                    # Check if the last two valid responses match
+                    if _check_sequence_responses_match(valid_responses_so_far[-2], valid_responses_so_far[-1]):
+                        log.info(f"Early match detected after {attempt + 1} attempts - sequences are consistent")
+                        # Add the matching response 4 more times to simulate consensus
+                        for _ in range(max_attempts - attempt - 1):
+                            responses.append(valid_responses_so_far[-1])
+                        break
             
         except Exception as e:
             log.warning(f"Sequence extraction attempt {attempt + 1} failed: {e}")
             responses.append(None)
-        
-        # Check for early consensus after 2 attempts
-        if len(responses) == 2:
-            if (responses[0] and responses[1] and 
-                _sequences_match(responses[0][1], responses[1][1])):
-                log.info("Sequence extraction consensus reached after 2 attempts")
-                return responses[0][0]  # Return original parsed data
-            else:
-                log.info("Sequence extraction mismatch after 2 attempts - trying third")
     
-    # After all attempts, use adaptive validation
+    # After all attempts, find most common sequences
     valid_responses = [r for r in responses if r is not None]
     
     if not valid_responses:
         log.error(f"All {max_attempts} sequence extraction attempts failed")
         return None
     
-    # First, try to find exact consensus (any matching pair)
-    for i in range(len(valid_responses)):
-        for j in range(i + 1, len(valid_responses)):
-            if _sequences_match(valid_responses[i][1], valid_responses[j][1]):
-                log.info(f"Sequence extraction consensus found: attempts with matching content")
-                return valid_responses[i][0]  # Return original parsed data
-    
-    # If no exact consensus, use adaptive validation
-    log.info("No exact consensus found, applying adaptive validation...")
-    
-    # Find sequences that appear consistently across multiple attempts
-    consistent_sequences = _find_consistent_sequences(valid_responses)
-    
-    if consistent_sequences:
-        log.info(f"Found {len(consistent_sequences)} consistent sequences using adaptive validation")
-        return consistent_sequences
-    
-    # If still no consensus, use the attempt with the most sequences
-    best_response = max(valid_responses, 
-                       key=lambda r: len(r[1]) if isinstance(r[1], list) else 0)
-    
-    if best_response and len(best_response[1]) > 0:
-        log.warning(f"No consensus after {max_attempts} attempts, using best effort with {len(best_response[1])} sequences")
-        return best_response[0]
-    
-    log.warning(f"Sequence extraction failed to find any valid sequences after {max_attempts} attempts")
-    return None
-
-
-def _find_consistent_sequences(valid_responses: List[Tuple[Any, List[Dict[str, Any]]]]) -> Optional[List[Dict[str, Any]]]:
-    """Find sequences that appear consistently across multiple extraction attempts.
-    
-    Args:
-        valid_responses: List of (original_data, normalized_data) tuples
-    
-    Returns:
-        List of consistent sequences with confidence scores, or None if none found
-    """
-    if not valid_responses:
-        return None
-    
-    # Count how many times each sequence appears
+    # Count occurrences of each individual sequence across all attempts
     sequence_counts = {}
-    sequence_full_data = {}
-    
-    for original, normalized in valid_responses:
-        if not isinstance(normalized, list):
-            continue
-            
-        for seq in normalized:
-            variant_id = seq.get("variant_id", "")
-            aa_seq = seq.get("aa_seq", "")
-            # Clean sequence before using in key
-            aa_seq_clean = aa_seq.replace(" ", "").replace("\n", "").upper() if aa_seq else ""
-            
-            # Create a unique key for this sequence
-            key = f"{variant_id}|{aa_seq_clean}"
-            
-            if key not in sequence_counts:
-                sequence_counts[key] = 0
-                sequence_full_data[key] = []
-            
-            sequence_counts[key] += 1
-            
-            # Find the full data for this sequence from the original response
-            if isinstance(original, list):
-                for orig_seq in original:
-                    if (orig_seq.get("variant_id") == variant_id and 
-                        orig_seq.get("aa_seq", "").replace(" ", "").replace("\n", "").upper() == aa_seq_clean):
-                        sequence_full_data[key].append(orig_seq)
-                        break
-    
-    # Filter sequences that appear in at least 2 attempts (40% of 5 attempts)
-    min_appearances = max(2, len(valid_responses) // 2)
-    consistent_sequences = []
-    
-    for key, count in sequence_counts.items():
-        if count >= min_appearances:
-            # Use the first occurrence of the full data
-            if sequence_full_data[key]:
-                seq_data = sequence_full_data[key][0].copy()
-                # Add confidence based on how many times it appeared
-                seq_data["confidence"] = count / len(valid_responses)
-                seq_data["extraction_consistency"] = f"{count}/{len(valid_responses)} attempts"
-                consistent_sequences.append(seq_data)
+    for resp in valid_responses:
+        if isinstance(resp, list):
+            for seq in resp:
+                if isinstance(seq, dict) and "variant_id" in seq:
+                    # Create a key for this sequence (variant_id + cleaned aa_seq)
+                    variant_id = seq.get("variant_id", "")
+                    aa_seq = seq.get("aa_seq", "")
+                    if aa_seq:
+                        aa_seq = aa_seq.replace(" ", "").replace("\n", "").upper()
+                    key = f"{variant_id}|{aa_seq}"
+                    
+                    if key not in sequence_counts:
+                        sequence_counts[key] = {"count": 0, "data": seq}
+                    sequence_counts[key]["count"] += 1
+    
+    # Build result with sequences that appear in at least 3 attempts
+    result = []
+    for key, info in sequence_counts.items():
+        if info["count"] >= 3:  # Appears in at least 3/6 attempts
+            seq_data = info["data"].copy()
+            seq_data["extraction_confidence"] = f"{info['count']}/{max_attempts}"
+            result.append(seq_data)
+            log.info(f"Sequence {seq_data.get('variant_id')} appeared in {info['count']}/{max_attempts} attempts")
+    
+    if result:
+        log.info(f"Extracted {len(result)} sequences with at least 3/{max_attempts} consensus")
+        return result
     
-    return consistent_sequences if consistent_sequences else None
+    # If no sequences appear twice, return the most complete attempt
+    best_attempt = max(valid_responses, key=lambda x: len(x) if isinstance(x, list) else 0)
+    log.warning(f"No consensus sequences found, returning best attempt with {len(best_attempt)} sequences")
+    return best_attempt
 
 
-def _normalize_sequence_response(data: Any) -> List[Dict[str, Any]]:
-    """Normalize sequence response for comparison."""
-    if not isinstance(data, list):
-        return []
-    
-    normalized = []
-    for item in data:
-        if isinstance(item, dict):
-            # Extract key fields for comparison
-            normalized_item = {
-                "variant_id": item.get("variant_id", ""),
-                "aa_seq": item.get("aa_seq", "").replace(" ", "").replace("\n", "").upper() if item.get("aa_seq") else "",
-                "dna_seq": item.get("dna_seq", "").replace(" ", "").replace("\n", "").upper() if item.get("dna_seq") else "",
-                "confidence": item.get("confidence", 0.0)
-            }
-            normalized.append(normalized_item)
-    
-    # Sort by variant_id for consistent comparison
-    return sorted(normalized, key=lambda x: x["variant_id"])
-
-
-def _sequences_match(seq1: List[Dict[str, Any]], seq2: List[Dict[str, Any]]) -> bool:
-    """Check if two sequence response lists match on key fields."""
-    if len(seq1) != len(seq2):
-        return False
-    
-    for i, (s1, s2) in enumerate(zip(seq1, seq2)):
-        # Compare variant IDs
-        if s1.get("variant_id") != s2.get("variant_id"):
-            return False
-        
-        # Compare amino acid sequences (most critical)
-        aa1 = s1.get("aa_seq", "")
-        aa2 = s2.get("aa_seq", "")
-        if aa1 and aa2 and aa1 != aa2:
-            return False
-        elif bool(aa1) != bool(aa2):  # One has sequence, other doesn't
-            return False
-        
-        # Compare DNA sequences if present
-        dna1 = s1.get("dna_seq", "")
-        dna2 = s2.get("dna_seq", "")
-        if dna1 and dna2 and dna1 != dna2:
-            return False
-    
-    return True
 
 
 def extract_sequences(text: str, model, *, debug_dir: str | Path | None = None, lineage_context: str = None, lineage_variants: List[Variant] = None) -> list[SequenceBlock]:
@@ -2624,18 +2537,7 @@ Match sequences to these known variants when possible. Variants may be labeled d
     else:
         prompt = base_prompt
     
-    # Add mutation validation context if we have lineage variants with mutations
-    if lineage_variants:
-        mutation_context = _build_mutation_validation_context(lineage_variants)
-        if mutation_context:
-            prompt = f"""{prompt}
-
-CRITICAL MUTATION VALIDATION:
-{mutation_context}
-
-IMPORTANT: Double-check your sequence assignments by verifying mutations match the lineage relationships.
-For example, if variant "III" has mutation "A100V" from parent "II", then position 100 in sequence "III" must be V, and position 100 in sequence "II" must be A.
-"""
+    # Skip mutation validation context
     
     # Save the complete prompt for debugging
     if debug_dir:
@@ -2662,11 +2564,7 @@ For example, if variant "III" has mutation "A100V" from parent "II", then positi
     
     extracted_sequences = _parse_sequences(data)
     
-    # Post-process: validate sequences against mutations if we have lineage info
-    if lineage_variants:
-        validated_sequences = _validate_sequences_against_mutations(extracted_sequences, lineage_variants, model, debug_dir)
-        return validated_sequences
-    
+    # Return extracted sequences without mutation validation
     return extracted_sequences
 
 # --- 7.4  JSON -> dataclass helpers -------------------------------------------
@@ -2701,6 +2599,19 @@ def _parse_sequences(raw: list[dict]) -> list[SequenceBlock]:
         aa  = _clean_seq(entry.get("aa_seq"),  _VALID_AA)
         dna = _clean_seq(entry.get("dna_seq"), _VALID_DNA)
 
+        # Check minimum length requirements
+        # AA sequences should be > 50, DNA sequences should be > 150
+        if aa and len(aa) <= 50:
+            log.debug(f"Skipping short AA sequence for {vid}: {len(aa)} amino acids")
+            aa = None
+        if dna and len(dna) <= 150:
+            log.debug(f"Skipping short DNA sequence for {vid}: {len(dna)} nucleotides")
+            dna = None
+
+        # Skip if both sequences are too short or missing
+        if not aa and not dna:
+            continue
+
         conf: float | None = None
         if aa:
             conf = sum(c in _VALID_AA  for c in aa)  / len(aa)
@@ -2943,12 +2854,15 @@ def get_sequences(text: str, model, *, pdf_paths: List[Path] = None, debug_dir:
                     validate_sequences=True
                 )
             
-            if focused_text and len(focused_text) < len(text):
-                log.info("Reduced text from %d to %d chars using validated location", 
-                         len(text), len(focused_text))
-            else:
-                log.warning("Failed to reduce text size - focused_text length: %d, full text length: %d", 
-                           len(focused_text) if focused_text else 0, len(text))
+            # Use focused text if we got any content, regardless of size
+            if focused_text:
+                if len(focused_text) < len(text):
+                    log.info("Reduced text from %d to %d chars using validated location", 
+                             len(text), len(focused_text))
+                else:
+                    log.info("Extracted focused text (%d chars) from validated location (full text: %d chars)", 
+                             len(focused_text), len(text))
+                
                 # Build lineage context if available
                 lineage_context = None
                 if lineage_variants:
@@ -2961,6 +2875,8 @@ def get_sequences(text: str, model, *, pdf_paths: List[Path] = None, debug_dir:
                     lineage_context = "\n".join(variant_info)
                 
                 return extract_sequences(focused_text, model, debug_dir=debug_dir, lineage_context=lineage_context, lineage_variants=lineage_variants)
+            else:
+                log.warning("Failed to extract focused text from validated location, will use full text")
         else:
             log.warning("Location validation failed or returned invalid location: %s", 
                        validation.get("reason", "Unknown"))
@@ -3113,12 +3029,6 @@ If you cannot determine certain fields, set them to null.
             seq = enzyme_info["wild_type_sequence"].upper().replace(" ", "").replace("\n", "")
             # Validate it looks like a protein sequence
             if seq and all(c in "ACDEFGHIKLMNPQRSTVWY*" for c in seq) and len(seq) > 50:
-                # Sanity check the sequence against known mutations
-                validated_seq = _validate_sequence_against_mutations(seq, variants, text, model)
-                if validated_seq:
-                    seq = validated_seq
-                    log.info(f"Sequence validated and potentially corrected by Gemini")
-                
                 # Map to the first variant or wild-type
                 wt_variant = next((v for v in variants if "WT" in v.variant_id.upper() or v.generation == 0), None)
                 if wt_variant:
@@ -3422,7 +3332,7 @@ def _merge_lineage_and_sequences(
     log.info(f"After direct merge: {merged_aa} variants with aa_seq, {merged_dna} with dna_seq")
     
     # 3. If we have unmatched sequences and a model, use Gemini to match
-    if model and len(df_seq) > 0 and df['aa_seq'].isna().any():
+    if model and len(df_seq) > 0 and (df['aa_seq'].isna().any() or df['dna_seq'].isna().any()):
         # Find unmatched entries - consider entries missing if they lack BOTH aa_seq and dna_seq
         missing_seq = df['aa_seq'].isna() & df['dna_seq'].isna()
         unmatched_lineage_ids = df[missing_seq]['variant_id'].tolist()
@@ -3437,14 +3347,9 @@ def _merge_lineage_and_sequences(
             log.info("Using Gemini to match variants")
             
             # Build prompt for Gemini
-            prompt = f"""Match enzyme variant IDs between two lists from the same paper.
+            prompt = f"""Match enzyme variant IDs between two lists from the same paper using your best judgment.
 
-Papers often use different naming conventions for the same variant:
-- Lineage sections may use numeric IDs (e.g., "5295") or IDs with parenthetical numbers (e.g., "ᴅ-G0 (5308)")
-- Sequence sections may use descriptive names (e.g., "ʟ-ApPgb-αEsA-G0", "ᴅ-ApPgb-αEsA-G0")
-
-Match variants by analyzing generation numbers, prefixes, and patterns. Some variant id are clearly mutations from a parent,
-use your best judgement to not match mutations to a parent even though they might share a substring in the variant id.
+These IDs come from different sections of the paper and may use different naming conventions for the same variant.
 
 Lineage variant IDs (need sequences):
 {json.dumps(unmatched_lineage_ids)}
@@ -3452,8 +3357,13 @@ Lineage variant IDs (need sequences):
 Sequence variant IDs (have sequences):
 {json.dumps(unmatched_seqs['variant_id'].tolist())}
 
+IMPORTANT: A variant with mutations (indicated by mutation codes like letters and numbers after an underscore or space) is a DIFFERENT enzyme from its parent. Do not match mutation variants to their base sequences - they are distinct entities with different sequences due to the mutations.
+
+Only match variants that represent the SAME enzyme, accounting for different naming conventions between sections.
+
 Return ONLY a JSON object mapping lineage IDs to sequence IDs.
 Format: {{"lineage_id": "sequence_id", ...}}
+Only include matches you are confident represent the same variant.
 """
             
             try:
@@ -3733,16 +3643,27 @@ def run_pipeline(
     # 4. Extract sequences (Section 7) ----------------------------------------
     sequences = get_sequences(full_text, model, pdf_paths=pdf_paths, debug_dir=debug_dir, lineage_variants=lineage)
     
-    # 4a. Try PDB extraction if no sequences found -----------------------------
-    # Check if we need PDB sequences (no sequences or only partial sequences)
-    MIN_PROTEIN_LENGTH = 50  # Most proteins are >50 AA
-    needs_pdb = (not sequences or 
-                 all(s.aa_seq is None or (s.aa_seq and len(s.aa_seq) < MIN_PROTEIN_LENGTH) 
-                     for s in sequences))
+    # 4a. First try to merge extracted sequences with lineage using Gemini matching
+    # This allows fuzzy matching of complex variant IDs before external lookups
+    doi = extract_doi(manuscript)
+    df_merged = merge_and_score(lineage, sequences, doi, model)
+    
+    # 4b. Check if ALL variants are missing sequences after merging
+    # Only try external sources if no sequences were successfully matched
+    all_missing_sequences = True
+    if 'aa_seq' in df_merged.columns or 'dna_seq' in df_merged.columns:
+        for _, row in df_merged.iterrows():
+            has_aa = pd.notna(row.get('aa_seq'))
+            has_dna = pd.notna(row.get('dna_seq'))
+            if has_aa or has_dna:
+                all_missing_sequences = False
+                break
     
-    if needs_pdb:
-        log.info("No full-length sequences found in paper (only partial sequences < %d AA), attempting PDB extraction...", 
-                 MIN_PROTEIN_LENGTH)
+    if all_missing_sequences:
+        MIN_PROTEIN_LENGTH = 50  # Most proteins are >50 AA
+        MIN_DNA_LENGTH = 150  # DNA sequences should be >150 nt
+        log.info("No full-length sequences found in paper (only partial sequences < %d AA or < %d nt), attempting PDB extraction...", 
+                 MIN_PROTEIN_LENGTH, MIN_DNA_LENGTH)
         
         # Extract PDB IDs from all PDFs
         pdb_ids = []
@@ -3780,7 +3701,13 @@ def run_pipeline(
                                 log.info(f"Added PDB sequence for {variant.variant_id} from {pdb_id}:{chain_id}")
                     
                     if pdb_seq_blocks:
-                        sequences = pdb_seq_blocks
+                        # Update the dataframe with PDB sequences
+                        for seq_block in pdb_seq_blocks:
+                            mask = df_merged['variant_id'] == seq_block.variant_id
+                            if mask.any():
+                                df_merged.loc[mask, 'aa_seq'] = seq_block.aa_seq
+                                df_merged.loc[mask, 'seq_confidence'] = seq_block.confidence
+                                df_merged.loc[mask, 'seq_source'] = seq_block.metadata.get('source', 'PDB')
                         log.info(f"Successfully extracted {len(pdb_seq_blocks)} sequences from PDB {pdb_id}")
                         break
                 else:
@@ -3788,8 +3715,15 @@ def run_pipeline(
         else:
             log.warning("No PDB IDs found in paper")
             
-        # 4b. If still no sequences, try Gemini extraction as last resort
-        if not sequences or all(not s.aa_seq for s in sequences):
+        # 4c. If still no sequences after PDB, try Gemini extraction as last resort
+        # Re-check if all variants are still missing sequences
+        still_all_missing = True
+        for _, row in df_merged.iterrows():
+            if pd.notna(row.get('aa_seq')) or pd.notna(row.get('dna_seq')):
+                still_all_missing = False
+                break
+        
+        if still_all_missing:
             log.info("No sequences from PDB, attempting Gemini-based extraction...")
             
             gemini_sequences = extract_enzyme_info_with_gemini(full_text, lineage, model)
@@ -3813,14 +3747,19 @@ def run_pipeline(
                         log.info(f"Added sequence for {variant.variant_id} via Gemini/UniProt: {len(seq)} residues")
                 
                 if gemini_seq_blocks:
-                    sequences = gemini_seq_blocks
+                    # Update the dataframe with Gemini/UniProt sequences
+                    for seq_block in gemini_seq_blocks:
+                        mask = df_merged['variant_id'] == seq_block.variant_id
+                        if mask.any():
+                            df_merged.loc[mask, 'aa_seq'] = seq_block.aa_seq
+                            df_merged.loc[mask, 'seq_confidence'] = seq_block.confidence
+                            df_merged.loc[mask, 'seq_source'] = seq_block.metadata.get('source', 'Gemini/UniProt')
                     log.info(f"Successfully extracted {len(gemini_seq_blocks)} sequences via Gemini")
             else:
                 log.warning("Failed to extract sequences via Gemini")
 
-    # 5. Merge & score (Section 8) --------------------------------------------
-    doi = extract_doi(manuscript)
-    df_final = merge_and_score(lineage, sequences, doi, model)
+    # 5. Use the merged dataframe (already merged above)
+    df_final = df_merged
 
     # 6. Write FINAL CSV -------------------------------------------------------
     if output_csv: