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public/scripts/interpro_annotation.sh

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+#!/bin/bash
+# Script name: run_interproscan.sh
+# Function: Batch process .faa files with InterProScan
+# Usage: ./run_interproscan.sh <input_directory> <output_directory>
+# Example: ./run_interproscan.sh ./input_genes ./ph_predict
+
+# Check input parameters (must be 2: input directory and output directory)
+if [ $# -ne 2 ]; then
+    echo "Error: Incorrect number of arguments!"
+    echo "Usage: $0 <input_directory> <output_directory>"
+    echo "Example: $0 ./prokka_annotation ./ph_predict"
+    exit 1
+fi
+
+input_dir="$1"
+output_root="$2"  # Output directory from parameter
+
+# Create main output directory
+echo "Creating main output directory: $output_root"
+mkdir -p "$output_root" || {
+    echo "Error: Failed to create output directory $output_root!"
+    exit 1
+}
+
+# Find all .faa files in input directory (including subdirectories)
+echo "Searching for .faa files in $input_dir..."
+FAA_FILES=$(find "$input_dir" -type f -name "*.faa")
+
+# Check if any .faa files were found
+if [ -z "$FAA_FILES" ]; then
+    echo "Error: No .faa files found in $input_dir (including subdirectories)!"
+    exit 1
+fi
+
+# Copy all .faa files to output directory
+echo "Copying .faa files to $output_root..."
+cp -v $FAA_FILES "$output_root/" || {
+    echo "Error: Failed to copy .faa files to $output_root!"
+    exit 1
+}
+
+# Process each .faa file with InterProScan
+echo "Starting InterProScan analysis..."
+for faa_file in "$output_root"/*.faa; do
+    # Skip if not a valid file (e.g., empty glob)
+    [ -f "$faa_file" ] || continue
+
+    # Extract sample name (remove path and .faa suffix)
+    sample_name=$(basename "$faa_file" .faa)
+    
+    # Define output files for this sample
+    # ips_output="${output_root}/${sample_name}_interproscan.tsv"  # InterProScan result
+    # filtered_output="${output_root}/${sample_name}_filtered.tsv"  # Filtered result
+    # gene_list="${output_root}/${sample_name}_gene_list.txt"        # Extracted gene names
+
+    echo "Processing $faa_file..."
+    # Run InterProScan (adjust parameters as needed; example uses common options)
+    /media/interproscan-5.75-106.0/interproscan.sh \
+        -i "$faa_file" \
+        -d "$output_root" \
+        -f tsv \
+        -cpu 8 \
+        -appl Pfam \
+        > "${output_root}/${sample_name}_ips.log" 2>&1
+
+    # Check if InterProScan succeeded
+    if [ $? -ne 0 ]; then
+        echo "Warning: InterProScan failed for $faa_file (see log: ${output_root}/${sample_name}_ips.log)"
+        continue
+    fi
+
+    # Filter results (example: retain rows with significance; adjust columns/conditions as needed)
+    # awk -F'\t' 'NR == 1 || $8 < 1e-5' "$ips_output" > "$filtered_output"
+
+    # Extract gene names (column 1 in InterProScan TSV)
+    # awk -F'\t' 'NR > 1 {print $1}' "$filtered_output" | sort -u > "$gene_list"
+
+    echo "Completed processing $sample_name:"
+    echo "  Raw results: $ips_output"
+    # echo "  Filtered results: $filtered_output"
+    # echo "  Gene list: $gene_list"
+done
+
+echo "All InterProScan analyses completed! Results in $output_root"