basic_usage.py

#!/usr/bin/env python3
"""
Basic usage examples for UMI RNA Simulator

This script demonstrates common simulation scenarios with synthetic data.
"""

from umi_simulator import BulkRNAUMISimulator


def basic_simulation():
    """Basic simulation with default parameters"""
    print("Example 1: Basic Simulation")
    print("-" * 60)

    simulator = BulkRNAUMISimulator(
        n_genes=1000,
        total_molecules=10000,
        random_seed=42
    )

    simulator.run_simulation(output_prefix="output/basic")


def high_amplification():
    """Simulation with high PCR amplification"""
    print("\nExample 2: High PCR Amplification")
    print("-" * 60)

    simulator = BulkRNAUMISimulator(
        n_genes=1000,
        total_molecules=10000,
        pcr_cycles=15,
        pcr_efficiency=0.85,
        random_seed=42
    )

    simulator.run_simulation(output_prefix="output/high_pcr")


def target_read_count():
    """Simulation using target read count instead of molecules"""
    print("\nExample 3: Target Read Count Mode")
    print("-" * 60)
    print("Requesting 50,000 final reads...")
    print("Simulator will back-calculate required initial molecules\n")

    simulator = BulkRNAUMISimulator(
        n_genes=1000,
        target_reads=50000,
        pcr_cycles=10,
        pcr_efficiency=0.7,
        random_seed=42
    )

    simulator.run_simulation(output_prefix="output/target_reads")


def paired_end_reads():
    """Simulation with paired-end reads"""
    print("\nExample 4: Paired-End Sequencing")
    print("-" * 60)

    simulator = BulkRNAUMISimulator(
        n_genes=1000,
        total_molecules=10000,
        paired_end=True,
        fragment_length=300,
        read_length=75,
        pcr_cycles=10,
        random_seed=42
    )

    simulator.run_simulation(output_prefix="output/paired_end")

    print("\nCreates two files:")
    print("  - output/paired_end_R1.fastq.gz (forward reads)")
    print("  - output/paired_end_R2.fastq.gz (reverse reads)")


if __name__ == '__main__':
    import os
    os.makedirs('output', exist_ok=True)

    print("="*70)
    print("UMI RNA Simulator - Basic Examples")
    print("="*70)

    basic_simulation()
    high_amplification()
    target_read_count()
    paired_end_reads()

    print("\n" + "="*70)
    print("All examples completed!")
    print("="*70)