--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scrappie_raw.py	Wed Aug 30 02:55:35 2017 -0400
@@ -0,0 +1,53 @@
+#!/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]
+
+    extract_fast5(tar_file)
+    with open(out_file, "w") as outfile:
+        subprocess.call(["scrappie",
+            "raw",
+            "--threads", threads,
+            "--outformat", "fasta",
+            "in_dir" ],
+            stdout=outfile )
+
+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')
+        for f in files:
+            shutil.copy(f, in_dir)
+
+    except OSError as e:
+        print("Unexpected error:", e.strerror)
+        raise
+
+    except:
+        print("Unexpected error:", sys.exc_info()[0])
+        raise
+
+if __name__ == "__main__" :
+    main()