Comprehensive Protein Analysis

from datetime import timedelta

## Initialize client
client = BioInfoToolsClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/17/BioInfo-Tools",
    "<your-api-key>"
)

if not await client.connect():
    print("connection failed")
    exit()

## Input: Protein sequence to analyze
protein_sequence = """
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
"""

sequence_id = "INS_HUMAN"

## Step 1, 2 & 3: Run comprehensive analysis (InterProScan + BLAST)
result = await client.session.call_tool(
    "analyze_protein",
    arguments={
        "sequence": protein_sequence.strip(),
        "sequence_id": sequence_id,
        "databases": ["Pfam"],     # InterProScan databases
        "evalue": 1e-5,             # BLAST E-value threshold (more stringent)
        "max_hits": 10              # BLAST max hits
    },
    read_timeout_seconds=timedelta(seconds=1200)  # Allow up to 20 minutes
)

## Step 4: Parse and display comprehensive results
result_data = client.parse_result(result)

print(f"{'='*80}")
print(f"Comprehensive Protein Analysis: {sequence_id}")
print(f"{'='*80}\n")

# InterProScan Results
ips_result = result_data.get("interproscan", {})
if ips_result.get("success"):
    ips_data = ips_result.get("results", {})
    domains = ips_data.get('domains', [])
    go_terms = ips_data.get('go_terms', [])

    print("=== DOMAIN ANALYSIS (InterProScan) ===")
    print(f"Execution time: {ips_result.get('time_seconds', '?')} seconds")
    print(f"Domains found: {len(domains)}")
    print(f"GO annotations: {len(go_terms)}\n")

    if domains:
        print("Functional Domains:")
        for domain in domains:
            print(f"  • {domain.get('name', 'N/A')} ({domain.get('database', 'N/A')})")
            if domain.get('description'):
                print(f"    Description: {domain.get('description')}")
            locations = domain.get('locations', [])
            if locations:
                loc = locations[0]
                print(f"    Position: {loc.get('start')}-{loc.get('end')} aa")
        print()

    if go_terms:
        print("Gene Ontology Annotations:")
        for go in go_terms[:5]:  # Show top 5
            print(f"  • {go.get('id', 'N/A')}: {go.get('name', 'N/A')}")
            print(f"    Category: {go.get('category', 'N/A')}")
        if len(go_terms) > 5:
            print(f"  ... and {len(go_terms) - 5} more")
        print()
else:
    print(f"❌ InterProScan failed: {ips_result.get('error', 'Unknown')}\n")

# BLAST Results
blast_result = result_data.get("blast", {})
if blast_result.get("success"):
    hits = blast_result.get('hits', [])

    print("=== HOMOLOGY SEARCH (BLAST) ===")
    print(f"Execution time: {blast_result.get('time_seconds', '?')} seconds")
    print(f"Similar sequences found: {blast_result.get('total_hits', 0)}")
    print(f"E-value threshold: {1e-5}\n")

    if hits:
        print("Top Homologous Proteins:")
        for i, hit in enumerate(hits[:5], 1):
            print(f"  {i}. {hit['uniprot_id']} - {hit.get('organism', 'N/A')}")
            print(f"     Description: {hit['description']}")
            print(f"     Identity: {hit['identity_percent']:.1f}%, E-value: {hit['evalue']:.2e}")
        if len(hits) > 5:
            print(f"  ... and {len(hits) - 5} more matches")
        print()
    else:
        print("No significant homologs found (E-value threshold may be too stringent)\n")
else:
    print(f"❌ BLAST failed: {blast_result.get('error', 'Unknown')}\n")

# Summary
print("=== FUNCTIONAL SUMMARY ===")
if domains:
    print(f"Protein Family: {domains[0].get('name', 'Unknown')}")
if hits:
    most_similar = hits[0]
    print(f"Most Similar Protein: {most_similar['uniprot_id']} ({most_similar['identity_percent']:.1f}% identity)")
    print(f"Organism: {most_similar.get('organism', 'Unknown')}")
print(f"{'='*80}")

await client.disconnect()