loop.sh

#!/bin/bash

# Configuration
SCRIPT_PATH="hubmap_dir_conversion_v3.6.py"
MICROSCOPE_HARDWARE=""
CUSTOM_PROBES_BED=""
TISSUE_BOUNDARY_DIR=""
BASE_OUT_DIR=""


# Array - populate with your input directory paths
inputs=(
)

# Validate required files and directories exist
if [ ! -f "$MICROSCOPE_HARDWARE" ]; then
    echo "Error: Microscope hardware file not found: $MICROSCOPE_HARDWARE"
    exit 1
fi

if [ ! -f "$CUSTOM_PROBES_BED" ]; then
    echo "Error: Custom probes BED file not found: $CUSTOM_PROBES_BED"
    exit 1
fi

if [ ! -f "$SCRIPT_PATH" ]; then
    echo "Error: Python script not found: $SCRIPT_PATH"
    exit 1
fi

if [ ! -d "$TISSUE_BOUNDARY_DIR" ]; then
    echo "Error: Tissue boundary directory not found: $TISSUE_BOUNDARY_DIR"
    exit 1
fi

# Process each sample
for i in "${!inputs[@]}"; do
    input_dir="${inputs[$i]}"

    # Extract sample name from input directory
    sample_name=$(basename "$input_dir")

    # Find corresponding tissue boundary file
    tissue_file=$(find "$TISSUE_BOUNDARY_DIR" -name "${sample_name}.tissue-boundary.geojson" -type f)

    output_dir=$BASE_OUT_DIR/$sample_name

    echo "Processing sample $((i+1))/${#inputs[@]}: $sample_name"
    echo "Input: $input_dir"
    echo "Output: $output_dir"

    # Validate input directory exists
    if [ ! -d "$input_dir" ]; then
        echo "Warning: Input directory not found: $input_dir"
        echo "Skipping..."
        continue
    fi

    # Check if tissue boundary file was found
    if [ -z "$tissue_file" ]; then
        echo "Warning: Tissue boundary file not found for sample: ${sample_name}.tissue-boundary.geojson"
        echo "Skipping..."
        continue
    fi

    # Check if multiple files were found (shouldn't happen but good to check)
    tissue_file_count=$(echo "$tissue_file" | wc -l)
    if [ "$tissue_file_count" -gt 1 ]; then
        echo "Warning: Multiple tissue boundary files found for sample: $sample_name"
        echo "$tissue_file"
        echo "Using first match..."
        tissue_file=$(echo "$tissue_file" | head -n1)
    fi

    echo "Tissue boundary: $tissue_file"

    # Run the Python script
    python "$SCRIPT_PATH" \
        --input "$input_dir" \
        --output "$output_dir" \
        --sample "$sample_name" \
        --microscope-hardware "$MICROSCOPE_HARDWARE" \
        --tissue-boundary "$tissue_file" \
        --custom-probes-bed "$CUSTOM_PROBES_BED" \
        --verbose

    # Check exit status
    if [ $? -eq 0 ]; then
        echo "Successfully processed: $sample_name"
    else
        echo "Error processing: $sample_name"
    fi

    echo "----------------------------------------"
done

echo "Processing complete!"