--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_assembly/mira.py	Tue Jun 07 16:23:51 2011 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+"""A simple wrapper script to call MIRA and collect its output.
+"""
+import os
+import sys
+import subprocess
+import shutil
+import time
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg+"\n")
+    sys.exit(err)
+
+def tcs_to_tabular(old, new):
+    in_handle = open(old, "rU")
+    out_handle = open(new, "w")
+    assert in_handle.readline() == "#TCS V1.0\n"
+    assert in_handle.readline() == "#\n"
+    assert in_handle.readline() == "# contig name          padPos  upadPos | B  Q | tcov covA covC covG covT cov* | qA qC qG qT q* |  S | Tags\n"
+    assert in_handle.readline() == "#\n"
+    out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q",
+                                         "tcov", "covA", "covC", "covG", "covT", "cov*",
+                                         "qA", "qC", "qG", "qT", "q*", "S", "Tags"]))
+    for line in in_handle:
+        parts = line.rstrip("\n").split(None,22)
+        assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|"
+        wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:]
+        out_handle.write("%s\n" % "\t".join(wanted))
+    out_handle.close()
+    in_handle.close()
+
+def collect_output(temp, name):
+    n3 = (temp, name, name, name)
+    tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)
+    for old, new in [("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta" % n3, out_fasta),
+                     ("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta.qual" % n3, out_qual),
+                     ("%s/%s_assembly/%s_d_results/%s_out.wig" % n3, out_wig),
+                     ("%s/%s_assembly/%s_d_results/%s_out.caf" % n3, out_caf),
+                     ("%s/%s_assembly/%s_d_results/%s_out.ace" % n3, out_ace)]:
+        if not os.path.isfile(old):
+            stop_err("Missing %s output file" % os.path.splitext(old)[-1])
+        else:
+            shutil.move(old, new)
+
+def clean_up(temp, name):
+    folder = "%s/%s_assembly" % (temp, name)
+    if os.path.isdir(folder):
+        shutil.rmtree(folder)
+
+#TODO - Run MIRA in /tmp or a configurable directory?
+temp = "."
+name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
+start_time = time.time()
+try:
+    cmd = " ".join(sys.argv[9:])
+    child = subprocess.Popen(sys.argv[9:],
+                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+except Exception, err:
+    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+run_time = time.time() - start_time
+return_code = child.returncode
+handle = open(out_log, "w")
+handle.write(stdout)
+handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
+print "MIRA took %0.2f minutes" % (run_time / 60.0)
+if return_code:
+    handle.write("Return error code %i from command:\n" % return_code)
+    handle.write(cmd + "\n")
+    handle.close()
+    clean_up(temp, name)
+    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+             return_code)
+handle.close()
+
+collect_output(temp, name)
+clean_up(temp, name)
+print "Done"