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models/mediaPredict.sh

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+#!/bin/bash
+# Script name: run_annotation_pipeline.sh
+# Function: Combine kofamscan annotation and Inference prediction
+# Usage: ./run_annotation_pipeline.sh <prokka_annotation_dir> <output_dir> <fasta_root_path>
+# Example: ./run_annotation_pipeline.sh ./prokka_annotation ./media_predict /home/gzy/uncultured/uncultivated_genome/uncultured_protein/
+
+# Check input parameters
+if [ $# -ne 2 ]; then
+    echo "Error: Incorrect number of arguments!"
+    echo "Usage: $0 <prokka_annotation_dir> <output_dir>"
+    echo "Example: $0 ./prokka_annotation ./media_predict"
+    exit 1
+fi
+
+# Assign parameters
+PROKKA_DIR="$1"
+OUTPUT_DIR="$2"
+FASTA_ROOT="$2"
+INFERENCE_SCRIPT="./scripts/Inference.py"
+DATA_PKL="./scripts/data.pkl"
+MODEL_PATH="./scripts/best_model.pt"
+ANNOTATION_SUFFIX="_ko.txt"
+
+# Create output directory
+echo "=== Creating output directory ==="
+mkdir -p "$OUTPUT_DIR" || {
+    echo "Error: Failed to create output directory $OUTPUT_DIR"
+    exit 1
+}
+
+# Step 1: Run kofamscan annotation
+echo -e "\n=== Step 1: Running kofamscan annotation ==="
+if [ -f "./scripts/kofamscan.sh" ]; then
+    bash ./scripts/kofamscan.sh "$PROKKA_DIR" "$OUTPUT_DIR" || {
+        echo "Error: kofamscan.sh execution failed"
+        exit 1
+    }
+else
+    echo "Error: kofamscan.sh not found in current directory"
+    exit 1
+fi
+
+# Check if annotation files were generated
+echo -e "\n=== Checking annotation results ==="
+annotation_files=$(find "$OUTPUT_DIR" -type f -name "*$ANNOTATION_SUFFIX")
+if [ -z "$annotation_files" ]; then
+    echo "Error: No annotation files (*$ANNOTATION_SUFFIX) found in $OUTPUT_DIR"
+    exit 1
+else
+    echo "Found $(echo "$annotation_files" | wc -l) annotation files. Proceeding to prediction..."
+fi
+
+# Step 2: Run Inference prediction
+echo -e "\n=== Step 2: Running Inference prediction ==="
+if [ -f "$INFERENCE_SCRIPT" ]; then
+    python "$INFERENCE_SCRIPT" \
+        --annotation_dir "$OUTPUT_DIR" \
+        --startswith "" \
+        --endswith "$ANNOTATION_SUFFIX" \
+        --fasta_path "$FASTA_ROOT" \
+        --data_pkl "$DATA_PKL" \
+        --model_path "$MODEL_PATH" \
+        --output_dir "$OUTPUT_DIR" \
+        --annotation_type kofamscan || {
+        echo "Error: Inference.py execution failed"
+        exit 1
+    }
+else
+    echo "Error: $INFERENCE_SCRIPT not found in current directory"
+    exit 1
+fi
+
+echo -e "\n=== All pipeline steps completed successfully ==="
+echo "Results are saved in: $OUTPUT_DIR"