--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy_core_wrapper.py	Fri Mar 08 20:46:56 2019 -0500
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+# --------------------------------------
+#
+#        snippy_core_wrapper.py
+#
+# This is an intermediary script between snippy-core.xml and snippy-core
+# It:
+#   - Copys the supplied zipped snippy output files to the working dir
+#   - Untars them to their datafile name
+#   - Builds the snippy-core command
+#   - Runs the snippy-core command
+#
+# --------------------------------------
+
+import argparse
+import os
+import subprocess
+from shutil import copyfile
+
+
+def main():
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
+    parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
+    args = parser.parse_args()
+
+    snippy_core_command_line = ['snippy-core', '--ref', args.ref]
+
+    for input_dataset in args.indirs.split(','):
+        base_name = os.path.basename(input_dataset)
+        copyfile(input_dataset, base_name)
+        subprocess.Popen(['tar', '-xf', base_name]).wait()
+
+    extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
+    for extracted_dir in extracted_dirs:
+        snippy_core_command_line.append(extracted_dir)
+
+    subprocess.Popen(snippy_core_command_line).wait()
+
+
+if __name__ == '__main__':
+    main()