diff test.py @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.py	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+from __future__ import division
+from __future__ import print_function
+import sys
+import argparse
+import subprocess
+
+OPT_DEFAULTS = {}
+USAGE = "%(prog)s [options]"
+DESCRIPTION = """"""
+
+
+def main(argv):
+
+  parser = argparse.ArgumentParser(description=DESCRIPTION)
+  parser.set_defaults(**OPT_DEFAULTS)
+
+  parser.add_argument('file1')
+  parser.add_argument('file2')
+
+  args = parser.parse_args(argv[1:])
+
+  """
+  cat $fastq1 | paste - - - - \
+    | paste - <(cat $fastq2 | paste - - - -) \
+    | awk -f make-barcodes.awk \
+    | sort \
+    | align_families.py \
+    | dunovo.py \
+    > $sscs
+  """
+
+  cmd1 = subprocess.Popen(['cat', args.file1], stdout=subprocess.PIPE)
+  cmd2 = subprocess.Popen(['cat', args.file2], stdout=subprocess.PIPE)
+
+
+def fail(message):
+  sys.stderr.write(message+"\n")
+  sys.exit(1)
+
+if __name__ == '__main__':
+  sys.exit(main(sys.argv))