Examples

This section provides comprehensive examples demonstrating how to use elsheeto to parse different types of sample sheets.

Overview

The examples demonstrate:

Basic parsing: Using the facade functions for simple parsing
Data extraction: Accessing header information, settings, and sample data
Platform-specific features: Handling unique features like Aviti’s composite indices
Real-world scenarios: Complete workflows from file to analysis

Each example includes:

Complete, runnable Python scripts
Step-by-step explanations
Sample data files
Expected output

Running the Examples

All examples are available in the examples/ directory of the elsheeto repository. You can run them directly:

# Run all examples and generate output files
make examples

# Or run individual examples
uv run python examples/read_illumina_v1.py
uv run python examples/read_aviti.py

The make examples command will create output files in examples/output/ showing the results of parsing each sample sheet type.

Advanced Configuration

Column Consistency Handling

elsheeto provides flexible handling of sample sheets with inconsistent column counts. This is particularly useful when working with real-world sample sheets that may have formatting inconsistencies.

from elsheeto import parse_illumina_v1
from elsheeto.parser.common import ColumnConsistency, ParserConfiguration
import warnings

# Default behavior: warnings for inconsistencies with automatic padding
sheet = parse_illumina_v1("samplesheet.csv")

# Silent padding (no warnings)
config = ParserConfiguration(column_consistency=ColumnConsistency.PAD)
sheet = parse_illumina_v1("samplesheet.csv", config=config)

# Strict validation (raises exceptions for inconsistencies)
config = ParserConfiguration(column_consistency=ColumnConsistency.STRICT_SECTIONED)
sheet = parse_illumina_v1("samplesheet.csv", config=config)

# Capture warnings programmatically
with warnings.catch_warnings(record=True) as w:
    warnings.simplefilter("always")
    sheet = parse_illumina_v1("samplesheet.csv")
    if w:
        for warning in w:
            print(f"Warning: {warning.message}")