added utility script for concatenating annotate output

aux/process_annotate_output.sh

@@ -0,0 +1,112 @@
+#!/bin/bash
+
+# Utility script for combining filt and filt_intersect output from starfish annotate
+# across multiple independent runs
+
+# Function to display help menu
+display_help() {
+    echo "Usage: $0 [OPTIONS]"
+    echo ""
+    echo "Utility script for combining filt and filt_intersect output from starfish annotate"
+    echo ""
+    echo "Options:"
+    echo "  -i, --input FILE        Input TSV file with genome codes in the first field (required)"
+    echo "  -a, --analysis PREFIX   Path to root analysis directory containing an output directory for each genome (required)"
+    echo "  -o, --output PREFIX     Path and Prefix for output files (required)"
+    echo "  -h, --help              Display this help menu"
+    echo ""
+    echo "Example:"
+    echo "  $0 -i ome2assembly.txt -a starfish_run1 -o all_annotations"
+}
+
+# Initialize variables
+INPUT_FILE=""
+ANALYSIS_PREFIX=""
+OUTPUT_PREFIX=""
+HELP=false
+
+# Parse command-line arguments
+while [[ $# -gt 0 ]]; do
+    key="$1"
+    case $key in
+        -i|--input)
+            INPUT_FILE="$2"
+            shift 2
+            ;;
+        -a|--analysis)
+            ANALYSIS_PREFIX="$2"
+            shift 2
+            ;;
+        -o|--output)
+            OUTPUT_PREFIX="$2"
+            shift 2
+            ;;
+        -h|--help)
+            HELP=true
+            shift
+            ;;
+        *)
+            echo "Unknown option: $1"
+            display_help
+            exit 1
+            ;;
+    esac
+done
+
+# Display help or validate required arguments
+if [[ "$HELP" = true ]] || [ -z "$INPUT_FILE" ] || [ -z "$ANALYSIS_PREFIX" ] || [ -z "$OUTPUT_PREFIX" ]; then
+    display_help
+    exit 1
+fi
+
+output_gff=${OUTPUT_PREFIX}.gff
+output_ids=${OUTPUT_PREFIX}.ids
+output_fas=${OUTPUT_PREFIX}.fas
+
+# Check if the input file exists
+if [ ! -f "$INPUT_FILE" ]; then
+    echo "Error: Input file $INPUT_FILE does not exist."
+    exit 1
+fi
+
+# Initialize counters
+count_filt_intersect=0
+count_filt=0
+count_none=0
+
+# Clear the output file or create it if it doesn't exist
+> "$output_gff"
+> "$output_ids"
+> "$output_fas"
+
+# Read each genome code from the input file
+while IFS=$'\t' read -r genome_code rest_of_line || [ -n "$genome_code" ]; do
+
+    # Trim any potential whitespace from the genome code
+    genome_code=$(echo "$genome_code" | xargs)
+
+    # Define the directory name based on the genome code
+    dir_name="${ANALYSIS_PREFIX}/$genome_code"
+
+    # Check for 'filt_intersect' file first
+    if [ -f "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt_intersect.ids" ]; then
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt_intersect.ids" >> "$output_ids"
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt_intersect.fas" >> "$output_fas"
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt_intersect.gff" >> "$output_gff"
+        ((count_filt_intersect++))
+    elif [ -f "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt.ids" ]; then
+        # If 'filt_intersect' doesn't exist, use 'filt' file
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt.ids" >> "$output_ids"
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt.fas" >> "$output_fas"
+        cat "${dir_name}/${genome_code}.${ANALYSIS_PREFIX}.filt.gff" >> "$output_gff"
+        ((count_filt++))
+    else
+        echo "No 'filt_intersect' or 'filt' file found for genome code: $genome_code"
+        ((count_none++))
+    fi
+done < "$INPUT_FILE"
+
+echo "Total genomes with 'filt_intersect' files: $count_filt_intersect"
+echo "Total genomes with 'filt' files: $count_filt"
+echo "Total genomes with no files: $count_none"
+echo "Processing complete"