--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_extract.py	Wed Sep 06 12:15:45 2017 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+
+import sys, os
+import glob
+import tarfile
+import subprocess
+import shutil
+import h5py
+import numpy as np
+
+def main():
+    tar_file = sys.argv[1]
+    out_file = sys.argv[2]
+    threads  = sys.argv[3] # currently unused
+
+    extract_fast5(tar_file)
+
+    subprocess.call(["nanopolish",
+		"extract",
+		"--recurse",
+        "--fastq",
+        "--output", out_file,
+        "in_dir" ])
+
+def extract_fast5(fn):
+
+    try:
+        in_dir = "in_dir"
+        if not os.path.exists(in_dir):
+            os.makedirs(in_dir)
+
+        tar = tarfile.open(fn, mode='r')
+        tar.extractall(path=in_dir)
+
+        files = glob.glob(
+            os.path.join(in_dir, "**", "*.fast5"),
+            recursive=True
+        )
+        if len(files) < 1:
+            raise ValueError('No FAST5 files found')
+
+    except OSError as e:
+        print("Unexpected error:", e.strerror)
+        raise
+
+    except:
+        print("Unexpected error:", sys.exc_info()[0])
+        raise
+
+if __name__ == "__main__" :
+    main()