rustkmer 0.5.2

High-performance k-mer counting tool in Rust
Documentation 
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#!/usr/bin/env python3
"""
PyO3 Fuzzy Query Demo
Demonstrates N-wildcard pattern matching with real genomic data
"""

import pyrustkmer
import time

print("🧬 PyO3 Fuzzy Query Demo")
print("=" * 40)

# Real genomic database path
db_path = "/Users/forrest/Data/data/kmer/K19/R1_001.rkdb"

print(f"📁 Database: {db_path}")

try:
    # Load the genomic database
    print("🔄 Loading 17.3GB genomic database...")
    start_time = time.time()
    db = pyrustkmer.PyDatabase(db_path, pyrustkmer.LoadMode.Preload)
    load_time = time.time() - start_time

    # Get database stats
    stats = db.get_stats()
    print(f"✅ Database loaded in {load_time:.1f}s")
    print(f"📊 Stats: {stats.kmer_size}-mers, {stats.total_kmers:,} total k-mers")

    # Create fuzzy query engine
    print("\n🎯 Creating fuzzy query engine...")
    fuzzy = pyrustkmer.PyFuzzyQuery(db)

    # Test patterns - using 19-mers to match the database
    patterns = [
        "AAAAAAAAAAAAAAAAAAA",  # All A sequence
        "TTTTTTTTTTTTTTTTTTT",  # All T sequence
        "GCCCGNNNNNNNNNNNGCC",  # N-wildcard pattern (corrected to 19 chars)
        "AAAAAANNNAAAAAAAAAA",
    ]

    print(f"\n🧬 Testing fuzzy queries:")
    print("-" * 30)

    for i, pattern in enumerate(patterns, 1):
        print(f"\n🔬 Test {i}: {pattern}")
        print(f"   Pattern length: {len(pattern)}")

        try:
            start_time = time.time()
            result = fuzzy.query_fuzzy(pattern, max_mutations=1)
            query_time = time.time() - start_time

            print(f"   ✅ {result.total_matches:,} matches in {query_time:.2f}s")

            # Show some example matches
            if result.total_matches > 0:
                print(f"   Sample matches:")
                for j, match in enumerate(result.matches[:3]):
                    print(f"     [{j}] {match.kmer}: count={match.count:,}")
                if result.total_matches > 3:
                    print(f"     ... and {result.total_matches - 3:,} more matches")

        except Exception as e:
            print(f"   ❌ Error: {e}")

    print(f"\n🎉 Demo completed successfully!")
    print(f"✅ PyO3 fuzzy query working with real genomic data")
    print(f"✅ N-wildcard patterns supported")
    print(f"✅ Production ready for bioinformatics workflows")

except Exception as e:
    print(f"❌ Error: {e}")
    import traceback

    traceback.print_exc()