92 lines
3.2 KiB
Bash
92 lines
3.2 KiB
Bash
#!/bin/bash
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# Script name: run_kofam_scan.sh
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# Function: Batch perform KO annotation using kofam_scan for .faa files
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# Usage: ./run_kofam_scan.sh <input_directory> <output_directory>
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# Example: ./run_kofam_scan.sh ./input_genes ./output_ko
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# Check input parameters (must be 2: input directory and output directory)
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if [ $# -ne 2 ]; then
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echo "Error: Incorrect number of arguments!"
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echo "Usage: $0 <input_directory> <output_directory>"
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echo "Example: $0 ./prokka_annotation ./media_predict_dir"
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exit 1
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fi
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input_dir="$1"
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output_root="$2" # Output directory from parameter
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# Define fixed parameters for kofam_scan (modify these according to your actual paths)
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# KOFAM_EXEC="exec_annotation" # Path to exec_annotation executable
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PROFILES_DIR="/mnt/profiles" # Path to database profiles directory
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KO_LIST="/mnt/ko_list" # Path to ko_list file
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CPU=20 # Number of threads
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TMP_DIR="." # Temporary file directory
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E_VALUE="1e-5" # E-value threshold
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OUTPUT_FORMAT="mapper" # Output format
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# Create main output directory
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echo "Creating main output directory: $output_root"
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mkdir -p "$output_root" || {
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echo "Error: Failed to create output directory $output_root!"
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exit 1
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}
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# Check if kofam_scan executable exists
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# if [ ! -f "$KOFAM_EXEC" ]; then
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# echo "Error: kofam_scan executable not found at $KOFAM_EXEC"
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# exit 1
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# fi
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# Find all .faa files in input directory (including subdirectories)
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echo "Searching for .faa files in $input_dir..."
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FAA_FILES=$(find "$input_dir" -type f -name "*.faa")
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# Check if any .faa files were found
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if [ -z "$FAA_FILES" ]; then
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echo "Error: No .faa files found in $input_dir (including subdirectories)!"
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exit 1
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fi
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# Copy all .faa files to output directory
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echo "Copying .faa files to $output_root..."
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cp -v $FAA_FILES "$output_root/" || {
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echo "Error: Failed to copy .faa files to $output_root!"
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exit 1
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}
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# Process each .faa file with kofam_scan
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echo "Starting kofam_scan annotation..."
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for faa_file in "$output_root"/*.faa; do
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# Skip if not a valid file (e.g., empty glob)
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[ -f "$faa_file" ] || continue
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# Extract sample name (remove path and .faa suffix)
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sample_name=$(basename "$faa_file" .faa)
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# Define output files for this sample
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ko_output="${output_root}/${sample_name}_ko.txt" # kofam_scan result
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ko_log="${output_root}/${sample_name}_ko.log" # Log file
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echo "Processing $faa_file..."
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# Run kofam_scan
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exec_annotation -p "$PROFILES_DIR" \
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-k "$KO_LIST" \
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--cpu "$CPU" \
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--tmp-dir "$TMP_DIR" \
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-E "$E_VALUE" \
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-f "$OUTPUT_FORMAT" \
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-o "$ko_output" \
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"$faa_file" > "$ko_log" 2>&1
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# Check if kofam_scan succeeded
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if [ $? -ne 0 ]; then
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echo "Warning: kofam_scan failed for $faa_file (see log: $ko_log)"
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continue
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fi
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echo "Completed processing $sample_name:"
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echo " Results: $ko_output"
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echo " Log: $ko_log"
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done
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echo "All kofam_scan analyses completed! Results in $output_root" |