--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_config_file.py	Wed Sep 29 21:30:31 2021 +0000
@@ -0,0 +1,27 @@
+import argparse
+
+
+description = ("This script will create a configuration file for samples \
+                to be run in Pindel")
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input_file", nargs="*",
+                    help="One or more alignment files")
+parser.add_argument("--insert_size", nargs="+",
+                    help="Expected Insert size")
+parser.add_argument("--sample_label", nargs="+",
+                    help="Sample label")
+parser.add_argument("--output_config_file",
+                    help="Output config file")
+args = parser.parse_args()
+
+template = "{input_file}\t{insert_size}\t{sample_label}\n"
+with open(args.output_config_file, "w") as output:
+    for input_file, insert_size, sample_label in zip(args.input_file,
+                                                     args.insert_size,
+                                                     args.sample_label):
+        config_line = template.format(input_file=input_file,
+                                      insert_size=insert_size,
+                                      sample_label=sample_label)
+        output.write(config_line)