@synsci/cli-darwin-x64 1.1.77 → 1.1.78

package/bin/skills/adaptyv/reference/examples.md

@@ -0,0 +1,913 @@
+# Code Examples
+
+## Setup and Authentication
+
+### Basic Setup
+
+```python
+import os
+import requests
+from dotenv import load_dotenv
+
+# Load environment variables
+load_dotenv()
+
+# Configuration
+API_KEY = os.getenv("ADAPTYV_API_KEY")
+BASE_URL = "https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws"
+
+# Standard headers
+HEADERS = {
+    "Authorization": f"Bearer {API_KEY}",
+    "Content-Type": "application/json"
+}
+
+def check_api_connection():
+    """Verify API connection and credentials"""
+    try:
+        response = requests.get(f"{BASE_URL}/organization/credits", headers=HEADERS)
+        response.raise_for_status()
+        print("✓ API connection successful")
+        print(f"  Credits remaining: {response.json()['balance']}")
+        return True
+    except requests.exceptions.HTTPError as e:
+        print(f"✗ API authentication failed: {e}")
+        return False
+```
+
+### Environment Setup
+
+Create a `.env` file:
+```bash
+ADAPTYV_API_KEY=your_api_key_here
+```
+
+Install dependencies:
+```bash
+uv pip install requests python-dotenv
+```
+
+## Experiment Submission
+
+### Submit Single Sequence
+
+```python
+def submit_single_experiment(sequence, experiment_type="binding", target_id=None):
+    """
+    Submit a single protein sequence for testing
+
+    Args:
+        sequence: Amino acid sequence string
+        experiment_type: Type of experiment (binding, expression, thermostability, enzyme_activity)
+        target_id: Optional target identifier for binding assays
+
+    Returns:
+        Experiment ID and status
+    """
+
+    # Format as FASTA
+    fasta_content = f">protein_sequence\n{sequence}\n"
+
+    payload = {
+        "sequences": fasta_content,
+        "experiment_type": experiment_type
+    }
+
+    if target_id:
+        payload["target_id"] = target_id
+
+    response = requests.post(
+        f"{BASE_URL}/experiments",
+        headers=HEADERS,
+        json=payload
+    )
+
+    response.raise_for_status()
+    result = response.json()
+
+    print(f"✓ Experiment submitted")
+    print(f"  Experiment ID: {result['experiment_id']}")
+    print(f"  Status: {result['status']}")
+    print(f"  Estimated completion: {result['estimated_completion']}")
+
+    return result
+
+# Example usage
+sequence = "MKVLWAALLGLLGAAAAFPAVTSAVKPYKAAVSAAVSKPYKAAVSAAVSKPYK"
+experiment = submit_single_experiment(sequence, experiment_type="expression")
+```
+
+### Submit Multiple Sequences (Batch)
+
+```python
+def submit_batch_experiment(sequences_dict, experiment_type="binding", metadata=None):
+    """
+    Submit multiple protein sequences in a single batch
+
+    Args:
+        sequences_dict: Dictionary of {name: sequence}
+        experiment_type: Type of experiment
+        metadata: Optional dictionary of additional information
+
+    Returns:
+        Experiment details
+    """
+
+    # Format all sequences as FASTA
+    fasta_content = ""
+    for name, sequence in sequences_dict.items():
+        fasta_content += f">{name}\n{sequence}\n"
+
+    payload = {
+        "sequences": fasta_content,
+        "experiment_type": experiment_type
+    }
+
+    if metadata:
+        payload["metadata"] = metadata
+
+    response = requests.post(
+        f"{BASE_URL}/experiments",
+        headers=HEADERS,
+        json=payload
+    )
+
+    response.raise_for_status()
+    result = response.json()
+
+    print(f"✓ Batch experiment submitted")
+    print(f"  Experiment ID: {result['experiment_id']}")
+    print(f"  Sequences: {len(sequences_dict)}")
+    print(f"  Status: {result['status']}")
+
+    return result
+
+# Example usage
+sequences = {
+    "variant_1": "MKVLWAALLGLLGAAA...",
+    "variant_2": "MKVLSAALLGLLGAAA...",
+    "variant_3": "MKVLAAALLGLLGAAA...",
+    "wildtype": "MKVLWAALLGLLGAAA..."
+}
+
+metadata = {
+    "project": "antibody_optimization",
+    "round": 3,
+    "notes": "Testing solubility-optimized variants"
+}
+
+experiment = submit_batch_experiment(sequences, "expression", metadata)
+```
+
+### Submit with Webhook Notification
+
+```python
+def submit_with_webhook(sequences_dict, experiment_type, webhook_url):
+    """
+    Submit experiment with webhook for completion notification
+
+    Args:
+        sequences_dict: Dictionary of {name: sequence}
+        experiment_type: Type of experiment
+        webhook_url: URL to receive notification when complete
+    """
+
+    fasta_content = ""
+    for name, sequence in sequences_dict.items():
+        fasta_content += f">{name}\n{sequence}\n"
+
+    payload = {
+        "sequences": fasta_content,
+        "experiment_type": experiment_type,
+        "webhook_url": webhook_url
+    }
+
+    response = requests.post(
+        f"{BASE_URL}/experiments",
+        headers=HEADERS,
+        json=payload
+    )
+
+    response.raise_for_status()
+    result = response.json()
+
+    print(f"✓ Experiment submitted with webhook")
+    print(f"  Experiment ID: {result['experiment_id']}")
+    print(f"  Webhook: {webhook_url}")
+
+    return result
+
+# Example
+webhook_url = "https://your-server.com/adaptyv-webhook"
+experiment = submit_with_webhook(sequences, "binding", webhook_url)
+```
+
+## Tracking Experiments
+
+### Check Experiment Status
+
+```python
+def check_experiment_status(experiment_id):
+    """
+    Get current status of an experiment
+
+    Args:
+        experiment_id: Experiment identifier
+
+    Returns:
+        Status information
+    """
+
+    response = requests.get(
+        f"{BASE_URL}/experiments/{experiment_id}",
+        headers=HEADERS
+    )
+
+    response.raise_for_status()
+    status = response.json()
+
+    print(f"Experiment: {experiment_id}")
+    print(f"  Status: {status['status']}")
+    print(f"  Created: {status['created_at']}")
+    print(f"  Updated: {status['updated_at']}")
+
+    if 'progress' in status:
+        print(f"  Progress: {status['progress']['percentage']}%")
+        print(f"  Current stage: {status['progress']['stage']}")
+
+    return status
+
+# Example
+status = check_experiment_status("exp_abc123xyz")
+```
+
+### List All Experiments
+
+```python
+def list_experiments(status_filter=None, limit=50):
+    """
+    List experiments with optional status filtering
+
+    Args:
+        status_filter: Filter by status (submitted, processing, completed, failed)
+        limit: Maximum number of results
+
+    Returns:
+        List of experiments
+    """
+
+    params = {"limit": limit}
+    if status_filter:
+        params["status"] = status_filter
+
+    response = requests.get(
+        f"{BASE_URL}/experiments",
+        headers=HEADERS,
+        params=params
+    )
+
+    response.raise_for_status()
+    result = response.json()
+
+    print(f"Found {result['total']} experiments")
+    for exp in result['experiments']:
+        print(f"  {exp['experiment_id']}: {exp['status']} ({exp['experiment_type']})")
+
+    return result['experiments']
+
+# Example - list all completed experiments
+completed_experiments = list_experiments(status_filter="completed")
+```
+
+### Poll Until Complete
+
+```python
+import time
+
+def wait_for_completion(experiment_id, check_interval=3600):
+    """
+    Poll experiment status until completion
+
+    Args:
+        experiment_id: Experiment identifier
+        check_interval: Seconds between status checks (default: 1 hour)
+
+    Returns:
+        Final status
+    """
+
+    print(f"Monitoring experiment {experiment_id}...")
+
+    while True:
+        status = check_experiment_status(experiment_id)
+
+        if status['status'] == 'completed':
+            print("✓ Experiment completed!")
+            return status
+        elif status['status'] == 'failed':
+            print("✗ Experiment failed")
+            return status
+
+        print(f"  Status: {status['status']} - checking again in {check_interval}s")
+        time.sleep(check_interval)
+
+# Example (not recommended - use webhooks instead!)
+# status = wait_for_completion("exp_abc123xyz", check_interval=3600)
+```
+
+## Retrieving Results
+
+### Download Experiment Results
+
+```python
+import json
+
+def download_results(experiment_id, output_dir="results"):
+    """
+    Download and parse experiment results
+
+    Args:
+        experiment_id: Experiment identifier
+        output_dir: Directory to save results
+
+    Returns:
+        Parsed results data
+    """
+
+    # Get results
+    response = requests.get(
+        f"{BASE_URL}/experiments/{experiment_id}/results",
+        headers=HEADERS
+    )
+
+    response.raise_for_status()
+    results = response.json()
+
+    # Save results JSON
+    os.makedirs(output_dir, exist_ok=True)
+    output_file = f"{output_dir}/{experiment_id}_results.json"
+
+    with open(output_file, 'w') as f:
+        json.dump(results, f, indent=2)
+
+    print(f"✓ Results downloaded: {output_file}")
+    print(f"  Sequences tested: {len(results['results'])}")
+
+    # Download raw data if available
+    if 'download_urls' in results:
+        for data_type, url in results['download_urls'].items():
+            print(f"  {data_type} available at: {url}")
+
+    return results
+
+# Example
+results = download_results("exp_abc123xyz")
+```
+
+### Parse Binding Results
+
+```python
+import pandas as pd
+
+def parse_binding_results(results):
+    """
+    Parse binding assay results into DataFrame
+
+    Args:
+        results: Results dictionary from API
+
+    Returns:
+        pandas DataFrame with organized results
+    """
+
+    data = []
+    for result in results['results']:
+        row = {
+            'sequence_id': result['sequence_id'],
+            'kd': result['measurements']['kd'],
+            'kd_error': result['measurements']['kd_error'],
+            'kon': result['measurements']['kon'],
+            'koff': result['measurements']['koff'],
+            'confidence': result['quality_metrics']['confidence'],
+            'r_squared': result['quality_metrics']['r_squared']
+        }
+        data.append(row)
+
+    df = pd.DataFrame(data)
+
+    # Sort by affinity (lower KD = stronger binding)
+    df = df.sort_values('kd')
+
+    print("Top 5 binders:")
+    print(df.head())
+
+    return df
+
+# Example
+experiment_id = "exp_abc123xyz"
+results = download_results(experiment_id)
+binding_df = parse_binding_results(results)
+
+# Export to CSV
+binding_df.to_csv(f"{experiment_id}_binding_results.csv", index=False)
+```
+
+### Parse Expression Results
+
+```python
+def parse_expression_results(results):
+    """
+    Parse expression testing results into DataFrame
+
+    Args:
+        results: Results dictionary from API
+
+    Returns:
+        pandas DataFrame with organized results
+    """
+
+    data = []
+    for result in results['results']:
+        row = {
+            'sequence_id': result['sequence_id'],
+            'yield_mg_per_l': result['measurements']['total_yield_mg_per_l'],
+            'soluble_fraction': result['measurements']['soluble_fraction_percent'],
+            'purity': result['measurements']['purity_percent'],
+            'percentile': result['ranking']['percentile']
+        }
+        data.append(row)
+
+    df = pd.DataFrame(data)
+
+    # Sort by yield
+    df = df.sort_values('yield_mg_per_l', ascending=False)
+
+    print(f"Mean yield: {df['yield_mg_per_l'].mean():.2f} mg/L")
+    print(f"Top performer: {df.iloc[0]['sequence_id']} ({df.iloc[0]['yield_mg_per_l']:.2f} mg/L)")
+
+    return df
+
+# Example
+results = download_results("exp_expression123")
+expression_df = parse_expression_results(results)
+```
+
+## Target Catalog
+
+### Search for Targets
+
+```python
+def search_targets(query, species=None, category=None):
+    """
+    Search the antigen catalog
+
+    Args:
+        query: Search term (protein name, UniProt ID, etc.)
+        species: Optional species filter
+        category: Optional category filter
+
+    Returns:
+        List of matching targets
+    """
+
+    params = {"search": query}
+    if species:
+        params["species"] = species
+    if category:
+        params["category"] = category
+
+    response = requests.get(
+        f"{BASE_URL}/targets",
+        headers=HEADERS,
+        params=params
+    )
+
+    response.raise_for_status()
+    targets = response.json()['targets']
+
+    print(f"Found {len(targets)} targets matching '{query}':")
+    for target in targets:
+        print(f"  {target['target_id']}: {target['name']}")
+        print(f"    Species: {target['species']}")
+        print(f"    Availability: {target['availability']}")
+        print(f"    Price: ${target['price_usd']}")
+
+    return targets
+
+# Example
+targets = search_targets("PD-L1", species="Homo sapiens")
+```
+
+### Request Custom Target
+
+```python
+def request_custom_target(target_name, uniprot_id=None, species=None, notes=None):
+    """
+    Request a custom antigen not in the standard catalog
+
+    Args:
+        target_name: Name of the target protein
+        uniprot_id: Optional UniProt identifier
+        species: Species name
+        notes: Additional requirements or notes
+
+    Returns:
+        Request confirmation
+    """
+
+    payload = {
+        "target_name": target_name,
+        "species": species
+    }
+
+    if uniprot_id:
+        payload["uniprot_id"] = uniprot_id
+    if notes:
+        payload["notes"] = notes
+
+    response = requests.post(
+        f"{BASE_URL}/targets/request",
+        headers=HEADERS,
+        json=payload
+    )
+
+    response.raise_for_status()
+    result = response.json()
+
+    print(f"✓ Custom target request submitted")
+    print(f"  Request ID: {result['request_id']}")
+    print(f"  Status: {result['status']}")
+
+    return result
+
+# Example
+request = request_custom_target(
+    target_name="Novel receptor XYZ",
+    uniprot_id="P12345",
+    species="Mus musculus",
+    notes="Need high purity for structural studies"
+)
+```
+
+## Complete Workflows
+
+### End-to-End Binding Assay
+
+```python
+def complete_binding_workflow(sequences_dict, target_id, project_name):
+    """
+    Complete workflow: submit sequences, track, and retrieve binding results
+
+    Args:
+        sequences_dict: Dictionary of {name: sequence}
+        target_id: Target identifier from catalog
+        project_name: Project name for metadata
+
+    Returns:
+        DataFrame with binding results
+    """
+
+    print("=== Starting Binding Assay Workflow ===")
+
+    # Step 1: Submit experiment
+    print("\n1. Submitting experiment...")
+    metadata = {
+        "project": project_name,
+        "target": target_id
+    }
+
+    experiment = submit_batch_experiment(
+        sequences_dict,
+        experiment_type="binding",
+        metadata=metadata
+    )
+
+    experiment_id = experiment['experiment_id']
+
+    # Step 2: Save experiment info
+    print("\n2. Saving experiment details...")
+    with open(f"{experiment_id}_info.json", 'w') as f:
+        json.dump(experiment, f, indent=2)
+
+    print(f"✓ Experiment {experiment_id} submitted")
+    print("  Results will be available in ~21 days")
+    print("  Use webhook or poll status for updates")
+
+    # Note: In practice, wait for completion before this step
+    # print("\n3. Waiting for completion...")
+    # status = wait_for_completion(experiment_id)
+
+    # print("\n4. Downloading results...")
+    # results = download_results(experiment_id)
+
+    # print("\n5. Parsing results...")
+    # df = parse_binding_results(results)
+
+    # return df
+
+    return experiment_id
+
+# Example
+antibody_variants = {
+    "variant_1": "EVQLVESGGGLVQPGG...",
+    "variant_2": "EVQLVESGGGLVQPGS...",
+    "variant_3": "EVQLVESGGGLVQPGA...",
+    "wildtype": "EVQLVESGGGLVQPGG..."
+}
+
+experiment_id = complete_binding_workflow(
+    antibody_variants,
+    target_id="tgt_pdl1_human",
+    project_name="antibody_affinity_maturation"
+)
+```
+
+### Optimization + Testing Pipeline
+
+```python
+# Combine computational optimization with experimental testing
+
+def optimization_and_testing_pipeline(initial_sequences, experiment_type="expression"):
+    """
+    Complete pipeline: optimize sequences computationally, then submit for testing
+
+    Args:
+        initial_sequences: Dictionary of {name: sequence}
+        experiment_type: Type of experiment
+
+    Returns:
+        Experiment ID for tracking
+    """
+
+    print("=== Optimization and Testing Pipeline ===")
+
+    # Step 1: Computational optimization
+    print("\n1. Computational optimization...")
+    from protein_optimization import complete_optimization_pipeline
+
+    optimized = complete_optimization_pipeline(initial_sequences)
+
+    print(f"✓ Optimization complete")
+    print(f"  Started with: {len(initial_sequences)} sequences")
+    print(f"  Optimized to: {len(optimized)} sequences")
+
+    # Step 2: Select top candidates
+    print("\n2. Selecting top candidates for testing...")
+    top_candidates = optimized[:50]  # Top 50
+
+    sequences_to_test = {
+        seq_data['name']: seq_data['sequence']
+        for seq_data in top_candidates
+    }
+
+    # Step 3: Submit for experimental validation
+    print("\n3. Submitting to Adaptyv...")
+    metadata = {
+        "optimization_method": "computational_pipeline",
+        "initial_library_size": len(initial_sequences),
+        "computational_scores": [s['combined'] for s in top_candidates]
+    }
+
+    experiment = submit_batch_experiment(
+        sequences_to_test,
+        experiment_type=experiment_type,
+        metadata=metadata
+    )
+
+    print(f"✓ Pipeline complete")
+    print(f"  Experiment ID: {experiment['experiment_id']}")
+
+    return experiment['experiment_id']
+
+# Example
+initial_library = {
+    f"variant_{i}": generate_random_sequence()
+    for i in range(1000)
+}
+
+experiment_id = optimization_and_testing_pipeline(
+    initial_library,
+    experiment_type="expression"
+)
+```
+
+### Batch Result Analysis
+
+```python
+def analyze_multiple_experiments(experiment_ids):
+    """
+    Download and analyze results from multiple experiments
+
+    Args:
+        experiment_ids: List of experiment identifiers
+
+    Returns:
+        Combined DataFrame with all results
+    """
+
+    all_results = []
+
+    for exp_id in experiment_ids:
+        print(f"Processing {exp_id}...")
+
+        # Download results
+        results = download_results(exp_id, output_dir=f"results/{exp_id}")
+
+        # Parse based on experiment type
+        exp_type = results.get('experiment_type', 'unknown')
+
+        if exp_type == 'binding':
+            df = parse_binding_results(results)
+            df['experiment_id'] = exp_id
+            all_results.append(df)
+
+        elif exp_type == 'expression':
+            df = parse_expression_results(results)
+            df['experiment_id'] = exp_id
+            all_results.append(df)
+
+    # Combine all results
+    combined_df = pd.concat(all_results, ignore_index=True)
+
+    print(f"\n✓ Analysis complete")
+    print(f"  Total experiments: {len(experiment_ids)}")
+    print(f"  Total sequences: {len(combined_df)}")
+
+    return combined_df
+
+# Example
+experiment_ids = [
+    "exp_round1_abc",
+    "exp_round2_def",
+    "exp_round3_ghi"
+]
+
+all_data = analyze_multiple_experiments(experiment_ids)
+all_data.to_csv("combined_results.csv", index=False)
+```
+
+## Error Handling
+
+### Robust API Wrapper
+
+```python
+import time
+from requests.exceptions import RequestException, HTTPError
+
+def api_request_with_retry(method, url, max_retries=3, backoff_factor=2, **kwargs):
+    """
+    Make API request with retry logic and error handling
+
+    Args:
+        method: HTTP method (GET, POST, etc.)
+        url: Request URL
+        max_retries: Maximum number of retry attempts
+        backoff_factor: Exponential backoff multiplier
+        **kwargs: Additional arguments for requests
+
+    Returns:
+        Response object
+
+    Raises:
+        RequestException: If all retries fail
+    """
+
+    for attempt in range(max_retries):
+        try:
+            response = requests.request(method, url, **kwargs)
+            response.raise_for_status()
+            return response
+
+        except HTTPError as e:
+            if e.response.status_code == 429:  # Rate limit
+                wait_time = backoff_factor ** attempt
+                print(f"Rate limited. Waiting {wait_time}s...")
+                time.sleep(wait_time)
+                continue
+
+            elif e.response.status_code >= 500:  # Server error
+                if attempt < max_retries - 1:
+                    wait_time = backoff_factor ** attempt
+                    print(f"Server error. Retrying in {wait_time}s...")
+                    time.sleep(wait_time)
+                    continue
+                else:
+                    raise
+
+            else:  # Client error (4xx) - don't retry
+                error_data = e.response.json() if e.response.content else {}
+                print(f"API Error: {error_data.get('error', {}).get('message', str(e))}")
+                raise
+
+        except RequestException as e:
+            if attempt < max_retries - 1:
+                wait_time = backoff_factor ** attempt
+                print(f"Request failed. Retrying in {wait_time}s...")
+                time.sleep(wait_time)
+                continue
+            else:
+                raise
+
+    raise RequestException(f"Failed after {max_retries} attempts")
+
+# Example usage
+response = api_request_with_retry(
+    "POST",
+    f"{BASE_URL}/experiments",
+    headers=HEADERS,
+    json={"sequences": fasta_content, "experiment_type": "binding"}
+)
+```
+
+## Utility Functions
+
+### Validate FASTA Format
+
+```python
+def validate_fasta(fasta_string):
+    """
+    Validate FASTA format and sequences
+
+    Args:
+        fasta_string: FASTA-formatted string
+
+    Returns:
+        Tuple of (is_valid, error_message)
+    """
+
+    lines = fasta_string.strip().split('\n')
+
+    if not lines:
+        return False, "Empty FASTA content"
+
+    if not lines[0].startswith('>'):
+        return False, "FASTA must start with header line (>)"
+
+    valid_amino_acids = set("ACDEFGHIKLMNPQRSTVWY")
+    current_header = None
+
+    for i, line in enumerate(lines):
+        if line.startswith('>'):
+            if not line[1:].strip():
+                return False, f"Line {i+1}: Empty header"
+            current_header = line[1:].strip()
+
+        else:
+            if current_header is None:
+                return False, f"Line {i+1}: Sequence before header"
+
+            sequence = line.strip().upper()
+            invalid = set(sequence) - valid_amino_acids
+
+            if invalid:
+                return False, f"Line {i+1}: Invalid amino acids: {invalid}"
+
+    return True, None
+
+# Example
+fasta = ">protein1\nMKVLWAALLG\n>protein2\nMATGVLWALG"
+is_valid, error = validate_fasta(fasta)
+
+if is_valid:
+    print("✓ FASTA format valid")
+else:
+    print(f"✗ FASTA validation failed: {error}")
+```
+
+### Format Sequences to FASTA
+
+```python
+def sequences_to_fasta(sequences_dict):
+    """
+    Convert dictionary of sequences to FASTA format
+
+    Args:
+        sequences_dict: Dictionary of {name: sequence}
+
+    Returns:
+        FASTA-formatted string
+    """
+
+    fasta_content = ""
+    for name, sequence in sequences_dict.items():
+        # Clean sequence (remove whitespace, ensure uppercase)
+        clean_seq = ''.join(sequence.split()).upper()
+
+        # Validate
+        is_valid, error = validate_fasta(f">{name}\n{clean_seq}")
+        if not is_valid:
+            raise ValueError(f"Invalid sequence '{name}': {error}")
+
+        fasta_content += f">{name}\n{clean_seq}\n"
+
+    return fasta_content
+
+# Example
+sequences = {
+    "var1": "MKVLWAALLG",
+    "var2": "MATGVLWALG"
+}
+
+fasta = sequences_to_fasta(sequences)
+print(fasta)
+```