From 1409d82b5bbf0ef10030283bbe4a1abfb65515c9 Mon Sep 17 00:00:00 2001
From: imsuneth <imsuneth@gmail.com>
Date: Thu, 21 May 2026 15:39:04 +1000
Subject: [PATCH] add script to compare freq bed with mmtsv

---
 test/compare_freq_bed_mmtsv.sh | 141 +++++++++++++++++++++++++++++++++
 1 file changed, 141 insertions(+)
 create mode 100755 test/compare_freq_bed_mmtsv.sh

diff --git a/test/compare_freq_bed_mmtsv.sh b/test/compare_freq_bed_mmtsv.sh
new file mode 100755
index 0000000..36fe0dc
--- /dev/null
+++ b/test/compare_freq_bed_mmtsv.sh
@@ -0,0 +1,141 @@
+#!/usr/bin/env bash
+#
+# Usage: ./compare_freq_bed_mmtsv.sh file1.bedmethyl file2.tsv output_dir
+#
+# This script compares two files based on a constructed key and outputs
+# the matched records, records with large differences, and records
+# missing in either file.
+
+usage() {
+    echo "Usage: $0 file1.bedmethyl file2.tsv output_dir"
+    echo "Options:"
+    echo "  -y : Overwrite existing output files without prompt."
+}
+
+# --- Parse Options ---
+while getopts ":y" opt; do
+    case $opt in
+        y)
+            OVERWRITE=true
+            ;;
+        \?)
+            echo "Invalid option: -$OPTARG" >&2
+            usage
+            exit 1
+            ;;
+    esac
+done
+shift $((OPTIND -1))
+
+# --- Configuration ---
+TOLERANCE=0.005 # Define the probability difference tolerance
+# --- Argument Check ---
+if [[ $# -ne 3 ]]; then
+    usage
+    exit 1
+fi
+f1=$1
+f2=$2
+out_dir=$3
+# # Check if extension of files are correct. file1 should be .bedmethyl or .bed and file2 should be .tsv
+# if [[ "$f1" != *.bedmethyl && "$f1" != *.bed ]] || [[ "$f2" != *.tsv ]]; then
+#     echo "Error: file1 should have .bedmethyl or .bed extension and file2 should have .tsv extension."
+#     exit 1
+# fi
+
+# Extract base names without extension
+base1=$(basename "$f1" .bedmethyl)
+if [[ "$f1" == *.bed ]]; then
+    base1=$(basename "$f1" .bed)
+fi
+base2=$(basename "$f2" .bed)
+
+
+mkdir -p "$out_dir"
+script_name=$(basename "$0" .sh)
+# --- Output Files ---
+OUT_MISSING_1="$out_dir/missing_in_file1.tsv" # Keys in file2 but not in file1
+OUT_MISSING_2="$out_dir/missing_in_file2.tsv" # Keys in file1 but not in file2
+OUT_MATCH="$out_dir/in_both.tsv"              # Keys in both with small prob difference
+OUT_LARGE_DIFF="$out_dir/large_freq_diff.tsv" # Keys in both with large freq difference
+# Remove output files if they already exist to avoid appending to old data. Ask for confirmation.
+if [[ -z "$OVERWRITE" && ( -f "$OUT_MISSING_1" || -f "$OUT_MISSING_2" || -f "$OUT_MATCH" || -f "$OUT_LARGE_DIFF" ) ]]; then
+    read -p "Output files already exist. Overwrite? (y/n) " choice
+    if [[ "$choice" != "y" ]]; then
+        echo "Exiting without overwriting files."
+        exit 1
+    fi
+fi
+rm -f "$OUT_MISSING_1" "$OUT_MISSING_2" "$OUT_MATCH" "$OUT_LARGE_DIFF"
+# --- AWK Processing ---
+awk -F'\t' -v tol="$TOLERANCE" \
+    -v out_match="$OUT_MATCH" \
+    -v out_large_diff="$OUT_LARGE_DIFF" \
+    -v out_missing1="$OUT_MISSING_1" \
+    -v out_missing2="$OUT_MISSING_2" '
+    # Helper function to trim whitespace and carriage returns
+    function clean(x) {
+        gsub(/\r/, "", x)
+        gsub(/^ +| +$/, "", x)
+        return x
+    }
+    # Set headers for output files at the beginning
+    BEGIN {
+        print "key\tprob\tdiff" > out_match
+        print "key\tdiff" > out_large_diff
+        print "key\tprob_file2" > out_missing1
+        print "key\tprob_file1" > out_missing2
+    }
+    # First pass: read file1 into an associative array `prob`
+    # NR==FNR is true only while reading the first file
+    NR==FNR {
+        for (i=1; i<=NF; i++) $i = clean($i)
+        # Construct the key from the first 6 columns
+        key = $1 "\t" $2 "\t" $4 "\t" $6
+        prob[key] = $11/100.0
+        next
+    }
+
+    # Second pass: process file2 and compare against the `prob` array
+    {
+        if (FNR == 1) next
+        for (i=1; i<=NF; i++) $i = clean($i)
+        # Construct the key from file2 columns in the order that matches file1
+        key1 = $1 "\t" $2 "\t" $8 "\t" $4
+        if (key1 in prob) {
+            # Key found in both files: calculate the difference
+            diff = prob[key1] - $7
+            if (diff < 0) diff = -diff # Absolute difference
+            if (diff <= tol) {
+                # Difference is within tolerance: write to matched.tsv
+                print key1 "\t" prob[key1] "\t" diff > out_match
+            } else {
+                # Difference is too large: write to large_prob_diff.tsv
+                print key1 "\t" diff > out_large_diff
+            }
+            # Delete the key from the array to mark it as found.
+            # At the end, only keys from file1 not in file2 will remain.
+            delete prob[key1]
+        } else {
+            # Key is in file2 but was not in file1
+            print key1 "\t" $7 > out_missing1
+        }
+    }
+    # END block: runs after all lines from all files have been processed
+    END {
+        # Any keys remaining in the `prob` array are from file1
+        # and were not found in file2.
+        for (key in prob) {
+            print key "\t" prob[key] > out_missing2
+        }
+    }
+' "$f1" "$f2"
+# --- Completion Message ---
+echo "Input files:"
+echo "  - file1: $f1"
+echo "  - file2: $f2"
+echo "Results written to:"
+echo "  - $OUT_MATCH"
+echo "  - $OUT_LARGE_DIFF"
+echo "  - $OUT_MISSING_1"
+echo "  - $OUT_MISSING_2"