Added script to compare sample ids

relecov_tools/__init__.py

@@ -1,5 +1,4 @@
-""" Main relecov package file.
-"""
+"""Main relecov package file."""
 
 import pkg_resources
 

relecov_tools/assets/compare_sampleids.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# Check if two arguments were provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <all_samples_file> <new_samples_file>"
+    exit 1
+fi
+
+# Assign arguments to variables
+all_samples_file="$1"
+new_samples_file="$2"
+
+# Check if the files exist
+if [ ! -f "$all_samples_file" ] || [ ! -f "$new_samples_file" ]; then
+    echo "Both files must exist."
+    exit 1
+fi
+
+# Find duplicates in the second file
+duplicates_in_new_file=$(sort "$new_samples_file" | uniq -d)
+
+if [ -n "$duplicates_in_new_file" ]; then
+    echo "New samples file contains duplicate samples. These samples are:"
+    echo "$duplicates_in_new_file"
+    exit 0
+fi
+
+# Find repeated samples between the two files
+duplicates=$(grep -Fxf "$all_samples_file" "$new_samples_file")
+
+if [ -n "$duplicates" ]; then
+    # If there are duplicate samples between the two files
+    echo "The second file contains samples that are already in the first file. These samples are:"
+    echo "$duplicates"
+else
+    # If all samples are new
+    echo "All samples have been added to the first file."
+    cat "$new_samples_file" >> "$all_samples_file"
+fi