CQall_plotter/run_from_cli.sh at main · neuropathbasel-pub/CQall_plotter · GitHub

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#!/bin/bash

# Script to run cqall_plotter from the command line with parameters

set -e

# Get the directory of this script
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m' # No Color

# Function to display usage
usage() {
    cat << EOF
${GREEN}Usage: $0 [OPTIONS]${NC}

${GREEN}Options:${NC}
    -m, --preprocessing_method METHOD
        Preprocessing method for summary plots (default: illumina)

    -c, --methylation_classes CLASSES
        Comma-separated list of methylation classes to plot
        Example: "BR_CA,IDH_HG,IDH_LG"

    -s, --min_sentrix_ids_per_plot NUMBER
        Minimum number of samples required per plot (default: 3)

    -p, --min_probes_per_bin NUMBER
        Minimum number of probes per bin

    -b, --bin_size SIZE
        Bin size for plotting

    -d, --downsize_to TARGET
        Downsizing target (default: NO_DOWNSIZING)

    -h, --help
        Display this help message

${GREEN}Examples:${NC}
    # Run with default settings
    $0

    # Run with specific methylation classes
    $0 --methylation_classes "BR_CA,IDH_HG"

    # Run with custom bin settings
    $0 --bin_size 50000 --min_probes_per_bin 20

    # Run with all options
    $0 -m illumina -c "BR_CA" -s 3 -b 50000 -p 20 -d NO_DOWNSIZING

EOF
}

# Parse arguments
PREPROCESSING_METHOD=""
METHYLATION_CLASSES=""
MIN_SENTRIX_IDS=""
MIN_PROBES_PER_BIN=""
BIN_SIZE=""
DOWNSIZE_TO=""

while [[ $# -gt 0 ]]; do
    case $1 in
        -m|--preprocessing_method)
            PREPROCESSING_METHOD="$2"
            shift 2
            ;;
        -c|--methylation_classes)
            METHYLATION_CLASSES="$2"
            shift 2
            ;;
        -s|--min_sentrix_ids_per_plot)
            MIN_SENTRIX_IDS="$2"
            shift 2
            ;;
        -p|--min_probes_per_bin)
            MIN_PROBES_PER_BIN="$2"
            shift 2
            ;;
        -b|--bin_size)
            BIN_SIZE="$2"
            shift 2
            ;;
        -d|--downsize_to)
            DOWNSIZE_TO="$2"
            shift 2
            ;;
        -h|--help)
            usage
            exit 0
            ;;
        *)
            echo -e "${RED}Unknown option: $1${NC}"
            usage
            exit 1
            ;;
    esac
done

# Check if virtual environment exists
if [ ! -d "$SCRIPT_DIR/.venv" ]; then
    echo -e "${RED}Error: Virtual environment not found at $SCRIPT_DIR/.venv${NC}"
    echo -e "${YELLOW}Please run 'uv sync' first to set up the environment${NC}"
    exit 1
fi

# Activate virtual environment
source "$SCRIPT_DIR/.venv/bin/activate"

# Build the Python command
PYTHON_CMD="python -m cqall_plotter.run_cqall_plotter"

# Add optional parameters
if [ -n "$PREPROCESSING_METHOD" ]; then
    PYTHON_CMD="$PYTHON_CMD --preprocessing_method $PREPROCESSING_METHOD"
fi

if [ -n "$METHYLATION_CLASSES" ]; then
    PYTHON_CMD="$PYTHON_CMD --methylation_classes $METHYLATION_CLASSES"
fi

if [ -n "$MIN_SENTRIX_IDS" ]; then
    PYTHON_CMD="$PYTHON_CMD --min_sentrix_ids_per_plot $MIN_SENTRIX_IDS"
fi

if [ -n "$MIN_PROBES_PER_BIN" ]; then
    PYTHON_CMD="$PYTHON_CMD --min_probes_per_bin $MIN_PROBES_PER_BIN"
fi

if [ -n "$BIN_SIZE" ]; then
    PYTHON_CMD="$PYTHON_CMD --bin_size $BIN_SIZE"
fi

if [ -n "$DOWNSIZE_TO" ]; then
    PYTHON_CMD="$PYTHON_CMD --downsize_to $DOWNSIZE_TO"
fi

# Display command being run
echo -e "${GREEN}Running:${NC}"
echo -e "${YELLOW}$PYTHON_CMD${NC}"
echo ""

# Run the Python script
eval "$PYTHON_CMD"