umi-bulk-rna-simulator/examples/advanced_usage.py at main · TheJacksonLaboratory/umi-bulk-rna-simulator · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
#!/usr/bin/env python3
"""
Advanced usage examples for UMI RNA Simulator

Demonstrates using real gene annotations (GTF) and genomic sequences (FASTA).
"""

from umi_simulator import BulkRNAUMISimulator


def bacterial_genome():
    """Example with bacterial genome (small, fast test)"""
    print("Example 1: Bacterial Genome (CP003773 - Mycoplasma)")
    print("-" * 60)

    gtf_file = "tests/data/CP003773.gtf"
    fasta_file = "tests/data/CP003773.fasta"

    if not os.path.exists(gtf_file) or not os.path.exists(fasta_file):
        print("ERROR: Test files not found in tests/data/")
        print("Please ensure test data is available.")
        return

    simulator = BulkRNAUMISimulator(
        gtf_file=gtf_file,
        fasta_file=fasta_file,
        total_molecules=5000,
        pcr_cycles=10,
        pcr_efficiency=0.7,
        random_seed=42
    )

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


def mouse_chromosome():
    """Example with mouse chromosome 19"""
    print("\nExample 2: Mouse Chromosome 19")
    print("-" * 60)

    gtf_file = "tests/data/GRCm39_chr19.gtf"
    fasta_file = "tests/data/GRCm39_chr19.fasta"

    if not os.path.exists(gtf_file) or not os.path.exists(fasta_file):
        print("ERROR: Mouse chr19 files not found")
        print("Run: cd tests/integration && bash extract_chr19_mouse.sh")
        return

    simulator = BulkRNAUMISimulator(
        gtf_file=gtf_file,
        fasta_file=fasta_file,
        total_molecules=20000,
        paired_end=True,
        fragment_length=300,
        read_length=75,
        pcr_cycles=10,
        pcr_efficiency=0.7,
        random_seed=42
    )

    simulator.run_simulation(output_prefix="output/mouse_chr19")


def custom_parameters():
    """Example with custom sequencing parameters"""
    print("\nExample 3: Custom Sequencing Parameters")
    print("-" * 60)

    simulator = BulkRNAUMISimulator(
        n_genes=500,
        total_molecules=10000,
        umi_length=12,
        read_length=150,
        sequencing_error_rate=0.005,  # 0.5% error rate
        umi_error_rate=0.01,           # 1% UMI error rate
        pcr_cycles=12,
        pcr_efficiency=0.75,
        random_seed=42
    )

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


def inline_umi():
    """Example with UMI in sequence instead of header"""
    print("\nExample 4: UMI In Sequence (inline)")
    print("-" * 60)
    print("UMI prepended to read sequence (matches some real protocols)\n")

    simulator = BulkRNAUMISimulator(
        n_genes=500,
        total_molecules=5000,
        umi_length=10,
        read_length=150,
        umi_in_sequence=True,  # UMI in sequence, not header
        pcr_cycles=8,
        random_seed=42
    )

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

    print("\nNote: Total read length = 150bp (10bp UMI + 140bp cDNA)")


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

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

    bacterial_genome()
    mouse_chromosome()
    custom_parameters()
    inline_umi()

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