Create SampleSeqGen.py

SampleSeqGen.py

@@ -0,0 +1,56 @@
+import csv
+from tkinter import filedialog
+import os
+
+# ZH 2024/04/10
+# inserts
+
+# assumes sample list is given as csv file with one sample name/id per line only
+
+
+def main():
+	"""Generates a partial sample sequence CSV file for use with S1Control & GeRDA system.
+	automates process of manually inserting CRM and Silica Blank breaks."""
+	path_to_sample_list_csv = filedialog.askopenfilename(
+		title="Select Sample Names CSV file",
+		filetypes=[("CSV File", "*.csv")],
+		initialdir=os.getcwd(),
+	)
+	number_samples_between_crms = int(input("Number of samples between CRMs: "))
+	number_of_crms = int(input("Number of CRMs to run each time: "))
+	crms = []
+	for i in range(1, number_of_crms + 1):
+		crms.append(input(f"Enter Name of CRM {i}: "))
+	crm_suffix_starting_num = int(
+		input(
+			"CRM suffix starting number (e.g. '4' = first crms will be named SiO2_004, etc. **if unsure, set to 1**): "
+		)
+	)
+	with open(path_to_sample_list_csv, "r") as sample_list_csv:
+		reader = csv.reader(sample_list_csv)
+		row_num = 0
+		new_sample_seq = []
+		for row in reader:
+			if row_num % number_samples_between_crms == 0:
+				for crm in crms:
+					new_sample_seq.append(
+						[f"{crm}_{str(crm_suffix_starting_num).zfill(4)}"]
+					)
+				crm_suffix_starting_num += 1
+			new_sample_seq.append(row)
+			row_num += 1
+		# then one final crm run at end
+		for crm in crms:
+			new_sample_seq.append([f"{crm}_{str(crm_suffix_starting_num).zfill(4)}"])
+
+	outputname = "sample_seq.csv"
+	with open(outputname, mode="x", newline="") as sample_seq_csv:
+		writer = csv.writer(sample_seq_csv)
+		writer.writerows(new_sample_seq)
+
+	print(f"sample sequence csv saved as '{outputname}'...")
+	input()
+
+
+if __name__ == "__main__":
+	main()