Add samplesheet checker #70

bin/samplesheetchecker.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+import csv
+import sys
+from pathlib import Path
+
+def check_file_exists(file_path):
+    return Path(file_path).is_file()
+
+def validate_samplesheet(samplesheet_path):
+    # Check if the samplesheet path is correct
+    if not Path(samplesheet_path).is_file():
+        print("Error: Invalid path to samplesheet.")
+        sys.exit(1)
+
+    # Open the samplesheet csv
+    with open(samplesheet_path, 'r') as file:
+        reader = csv.reader(file)
+        headers = next(reader)  # Read the header
+
+        # Check if the header matches the expected format
+        expected_header = ['sample', 'bam', 'bai']
+        if headers != expected_header:
+            print("Error: Invalid header format.")
+            sys.exit(1)
+
+        # Check columns for all rows are csv
+        for row in reader:
+            for column in row:
+                if '\t' in column:
+                    print("Error: Found a column with a tab delimiter, expected csv.")
+                    sys.exit(1)
+
+def modify_samplesheet(samplesheet_path):
+    output_csv = sys.argv[2]
+    output_header = ['sample', 'bam', 'bai']
+
+    with open(samplesheet_path, 'r') as file:
+        reader = csv.reader(file)
+        headers = next(reader)  # Read the header
+
+        rows = []
+        for row in reader:
+            bam = row[1]
+            bai = row[2]
+
+    with open(output_csv, 'w', newline='') as csvfile:
+        writer = csv.writer(csvfile)
+        writer.writerow(output_header)
+        writer.writerows(rows)
+
+def main():
+    input_csv = sys.argv[1]
+
+    # Validate samplesheet
+    validate_samplesheet(input_csv)
+
+    # Modify samplesheet
+    modify_samplesheet(input_csv)
+
+if __name__ == "__main__":
+    main()