Data Loading Project

A minimal project for loading and filtering gene expression data using Python and Pixi.

Setup

Install Pixi from pixi.sh, then run:

pixi install

Usage

Load and filter the gene expression dataset using a codebook:

pixi run python load_data.py ./originals/reference/DevVIS_p13_subset.csv ./originals/reference/codebook_73g_ctx.txt

Optionally specify an output path:

pixi run python load_data.py ./originals/reference/DevVIS_p13_subset.csv ./originals/reference/codebook_73g_ctx.txt -o ./output/filtered_genes.csv

Arguments

• csv_file: Path to the reference gene expression CSV file (required)
• codebook_file: Path to the codebook file containing gene names to keep (required)
• -o, --output: Path to save the filtered dataframe. Defaults to filtered_genes.csv in the CSV file's directory (optional)

This will:

• Load gene expression data from the CSV file
• Extract gene names from the codebook file (first column before tab character)
• Filter the dataframe to keep only genes listed in the codebook
• Reorder genes to match the codebook order
• Display the number of genes loaded, filtered shape, and data preview
• Save the filtered data to the specified output path (or default location)

Quick Start

Run the automated script:

bash run.sh