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Zhongwei Li
353
skills/pydeseq2/scripts/run_deseq2_analysis.py
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353
skills/pydeseq2/scripts/run_deseq2_analysis.py
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#!/usr/bin/env python3
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"""
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PyDESeq2 Analysis Script
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This script performs a complete differential expression analysis using PyDESeq2.
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It can be used as a template for standard RNA-seq DEA workflows.
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Usage:
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python run_deseq2_analysis.py --counts counts.csv --metadata metadata.csv \
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--design "~condition" --contrast condition treated control \
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--output results/
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Requirements:
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- pydeseq2
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- pandas
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- matplotlib (optional, for plots)
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"""
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import argparse
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import os
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import pickle
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import sys
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from pathlib import Path
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import pandas as pd
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try:
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from pydeseq2.dds import DeseqDataSet
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from pydeseq2.ds import DeseqStats
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except ImportError:
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print("Error: pydeseq2 not installed. Install with: pip install pydeseq2")
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sys.exit(1)
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def load_and_validate_data(counts_path, metadata_path, transpose_counts=True):
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"""Load count matrix and metadata, perform basic validation."""
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print(f"Loading count data from {counts_path}...")
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counts_df = pd.read_csv(counts_path, index_col=0)
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if transpose_counts:
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print("Transposing count matrix to samples × genes format...")
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counts_df = counts_df.T
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print(f"Loading metadata from {metadata_path}...")
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metadata = pd.read_csv(metadata_path, index_col=0)
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print(f"\nData loaded:")
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print(f" Counts shape: {counts_df.shape} (samples × genes)")
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print(f" Metadata shape: {metadata.shape} (samples × variables)")
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# Validate
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if not all(counts_df.index == metadata.index):
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print("\nWarning: Sample indices don't match perfectly. Taking intersection...")
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common_samples = counts_df.index.intersection(metadata.index)
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counts_df = counts_df.loc[common_samples]
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metadata = metadata.loc[common_samples]
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print(f" Using {len(common_samples)} common samples")
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# Check for negative or non-integer values
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if (counts_df < 0).any().any():
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raise ValueError("Count matrix contains negative values")
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return counts_df, metadata
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def filter_data(counts_df, metadata, min_counts=10, condition_col=None):
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"""Filter low-count genes and samples with missing data."""
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print(f"\nFiltering data...")
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initial_genes = counts_df.shape[1]
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initial_samples = counts_df.shape[0]
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# Filter genes
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genes_to_keep = counts_df.columns[counts_df.sum(axis=0) >= min_counts]
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counts_df = counts_df[genes_to_keep]
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genes_removed = initial_genes - counts_df.shape[1]
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print(f" Removed {genes_removed} genes with < {min_counts} total counts")
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# Filter samples with missing condition data
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if condition_col and condition_col in metadata.columns:
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samples_to_keep = ~metadata[condition_col].isna()
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counts_df = counts_df.loc[samples_to_keep]
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metadata = metadata.loc[samples_to_keep]
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samples_removed = initial_samples - counts_df.shape[0]
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if samples_removed > 0:
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print(f" Removed {samples_removed} samples with missing '{condition_col}' data")
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print(f" Final data shape: {counts_df.shape[0]} samples × {counts_df.shape[1]} genes")
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return counts_df, metadata
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def run_deseq2(counts_df, metadata, design, n_cpus=1):
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"""Run DESeq2 normalization and fitting."""
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print(f"\nInitializing DeseqDataSet with design: {design}")
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dds = DeseqDataSet(
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counts=counts_df,
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metadata=metadata,
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design=design,
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refit_cooks=True,
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n_cpus=n_cpus,
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quiet=False
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)
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print("\nRunning DESeq2 pipeline...")
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print(" Step 1/7: Computing size factors...")
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print(" Step 2/7: Fitting genewise dispersions...")
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print(" Step 3/7: Fitting dispersion trend curve...")
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print(" Step 4/7: Computing dispersion priors...")
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print(" Step 5/7: Fitting MAP dispersions...")
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print(" Step 6/7: Fitting log fold changes...")
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print(" Step 7/7: Calculating Cook's distances...")
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dds.deseq2()
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print("\n✓ DESeq2 fitting complete")
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return dds
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def run_statistical_tests(dds, contrast, alpha=0.05, shrink_lfc=True):
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"""Perform Wald tests and compute p-values."""
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print(f"\nPerforming statistical tests...")
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print(f" Contrast: {contrast}")
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print(f" Significance threshold: {alpha}")
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ds = DeseqStats(
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dds,
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contrast=contrast,
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alpha=alpha,
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cooks_filter=True,
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independent_filter=True,
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quiet=False
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)
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print("\n Running Wald tests...")
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print(" Filtering outliers based on Cook's distance...")
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print(" Applying independent filtering...")
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print(" Adjusting p-values (Benjamini-Hochberg)...")
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ds.summary()
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print("\n✓ Statistical testing complete")
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# Optional LFC shrinkage
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if shrink_lfc:
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print("\nApplying LFC shrinkage for visualization...")
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ds.lfc_shrink()
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print("✓ LFC shrinkage complete")
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return ds
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def save_results(ds, dds, output_dir, shrink_lfc=True):
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"""Save results and intermediate objects."""
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output_dir = Path(output_dir)
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output_dir.mkdir(parents=True, exist_ok=True)
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print(f"\nSaving results to {output_dir}/")
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# Save statistical results
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results_path = output_dir / "deseq2_results.csv"
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ds.results_df.to_csv(results_path)
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print(f" Saved: {results_path}")
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# Save significant genes
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significant = ds.results_df[ds.results_df.padj < 0.05]
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sig_path = output_dir / "significant_genes.csv"
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significant.to_csv(sig_path)
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print(f" Saved: {sig_path} ({len(significant)} significant genes)")
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# Save sorted results
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sorted_results = ds.results_df.sort_values("padj")
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sorted_path = output_dir / "results_sorted_by_padj.csv"
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sorted_results.to_csv(sorted_path)
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print(f" Saved: {sorted_path}")
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# Save DeseqDataSet as pickle
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dds_path = output_dir / "deseq_dataset.pkl"
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with open(dds_path, "wb") as f:
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pickle.dump(dds.to_picklable_anndata(), f)
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print(f" Saved: {dds_path}")
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# Print summary
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print(f"\n{'='*60}")
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print("ANALYSIS SUMMARY")
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print(f"{'='*60}")
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print(f"Total genes tested: {len(ds.results_df)}")
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print(f"Significant genes (padj < 0.05): {len(significant)}")
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print(f"Upregulated: {len(significant[significant.log2FoldChange > 0])}")
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print(f"Downregulated: {len(significant[significant.log2FoldChange < 0])}")
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print(f"{'='*60}")
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# Show top genes
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print("\nTop 10 most significant genes:")
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print(sorted_results.head(10)[["baseMean", "log2FoldChange", "pvalue", "padj"]])
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return results_path
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def create_plots(ds, output_dir):
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"""Create basic visualization plots."""
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try:
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import matplotlib.pyplot as plt
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import numpy as np
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except ImportError:
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print("\nNote: matplotlib not installed. Skipping plot generation.")
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return
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output_dir = Path(output_dir)
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results = ds.results_df.copy()
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print("\nGenerating plots...")
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# Volcano plot
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results["-log10(padj)"] = -np.log10(results.padj.fillna(1))
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plt.figure(figsize=(10, 6))
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significant = results.padj < 0.05
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plt.scatter(
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results.loc[~significant, "log2FoldChange"],
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results.loc[~significant, "-log10(padj)"],
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alpha=0.3, s=10, c='gray', label='Not significant'
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)
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plt.scatter(
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results.loc[significant, "log2FoldChange"],
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results.loc[significant, "-log10(padj)"],
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alpha=0.6, s=10, c='red', label='Significant (padj < 0.05)'
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)
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plt.axhline(-np.log10(0.05), color='blue', linestyle='--', linewidth=1, alpha=0.5)
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plt.axvline(1, color='gray', linestyle='--', linewidth=1, alpha=0.5)
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plt.axvline(-1, color='gray', linestyle='--', linewidth=1, alpha=0.5)
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plt.xlabel("Log2 Fold Change", fontsize=12)
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plt.ylabel("-Log10(Adjusted P-value)", fontsize=12)
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plt.title("Volcano Plot", fontsize=14, fontweight='bold')
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plt.legend()
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plt.tight_layout()
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volcano_path = output_dir / "volcano_plot.png"
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plt.savefig(volcano_path, dpi=300)
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plt.close()
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print(f" Saved: {volcano_path}")
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# MA plot
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plt.figure(figsize=(10, 6))
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plt.scatter(
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np.log10(results.loc[~significant, "baseMean"] + 1),
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results.loc[~significant, "log2FoldChange"],
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alpha=0.3, s=10, c='gray', label='Not significant'
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)
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plt.scatter(
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np.log10(results.loc[significant, "baseMean"] + 1),
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results.loc[significant, "log2FoldChange"],
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alpha=0.6, s=10, c='red', label='Significant (padj < 0.05)'
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)
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plt.axhline(0, color='blue', linestyle='--', linewidth=1, alpha=0.5)
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plt.xlabel("Log10(Base Mean + 1)", fontsize=12)
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plt.ylabel("Log2 Fold Change", fontsize=12)
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plt.title("MA Plot", fontsize=14, fontweight='bold')
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plt.legend()
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plt.tight_layout()
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ma_path = output_dir / "ma_plot.png"
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plt.savefig(ma_path, dpi=300)
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plt.close()
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print(f" Saved: {ma_path}")
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def main():
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parser = argparse.ArgumentParser(
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description="Run PyDESeq2 differential expression analysis",
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Basic analysis
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python run_deseq2_analysis.py \\
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--counts counts.csv \\
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--metadata metadata.csv \\
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--design "~condition" \\
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--contrast condition treated control \\
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--output results/
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# Multi-factor analysis
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python run_deseq2_analysis.py \\
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--counts counts.csv \\
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--metadata metadata.csv \\
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--design "~batch + condition" \\
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--contrast condition treated control \\
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--output results/ \\
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--n-cpus 4
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"""
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)
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parser.add_argument("--counts", required=True, help="Path to count matrix CSV file")
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parser.add_argument("--metadata", required=True, help="Path to metadata CSV file")
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parser.add_argument("--design", required=True, help="Design formula (e.g., '~condition')")
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parser.add_argument("--contrast", nargs=3, required=True,
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metavar=("VARIABLE", "TEST", "REFERENCE"),
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help="Contrast specification: variable test_level reference_level")
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parser.add_argument("--output", default="results", help="Output directory (default: results)")
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parser.add_argument("--min-counts", type=int, default=10,
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help="Minimum total counts for gene filtering (default: 10)")
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parser.add_argument("--alpha", type=float, default=0.05,
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help="Significance threshold (default: 0.05)")
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parser.add_argument("--no-transpose", action="store_true",
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help="Don't transpose count matrix (use if already samples × genes)")
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parser.add_argument("--no-shrink", action="store_true",
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help="Skip LFC shrinkage")
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parser.add_argument("--n-cpus", type=int, default=1,
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help="Number of CPUs for parallel processing (default: 1)")
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parser.add_argument("--plots", action="store_true",
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help="Generate volcano and MA plots")
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args = parser.parse_args()
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# Load data
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counts_df, metadata = load_and_validate_data(
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args.counts,
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args.metadata,
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transpose_counts=not args.no_transpose
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)
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# Filter data
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condition_col = args.contrast[0]
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counts_df, metadata = filter_data(
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counts_df,
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metadata,
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min_counts=args.min_counts,
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condition_col=condition_col
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)
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# Run DESeq2
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dds = run_deseq2(counts_df, metadata, args.design, n_cpus=args.n_cpus)
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# Statistical testing
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ds = run_statistical_tests(
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dds,
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contrast=args.contrast,
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alpha=args.alpha,
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shrink_lfc=not args.no_shrink
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)
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# Save results
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save_results(ds, dds, args.output, shrink_lfc=not args.no_shrink)
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# Create plots if requested
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if args.plots:
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create_plots(ds, args.output)
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print(f"\n✓ Analysis complete! Results saved to {args.output}/")
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if __name__ == "__main__":
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main()
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