--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4/mira4_bait.py	Fri Nov 21 06:42:56 2014 -0500
@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+"""A simple wrapper script to call MIRA4's mirabait and collect its output.
+"""
+import os
+import sys
+import subprocess
+import shutil
+import time
+
+WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg+"\n")
+    sys.exit(err)
+
+
+def get_version(mira_binary):
+    """Run MIRA to find its version number"""
+    # At the commend line I would use: mira -v | head -n 1
+    # however there is some pipe error when doing that here.
+    cmd = [mira_binary, "-v"]
+    try:
+        child = subprocess.Popen(cmd,
+                                 stdout=subprocess.PIPE,
+                                 stderr=subprocess.STDOUT)
+    except Exception, err:
+        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys.exit(1)
+    ver, tmp = child.communicate()
+    del child
+    #Workaround for -v not working in mirabait 4.0RC4
+    if "invalid option" in ver.split("\n", 1)[0]:
+        for line in ver.split("\n", 1):
+            if " version " in line:
+                line = line.split()
+                return line[line.index("version")+1].rstrip(")")
+        stop_err("Could not determine MIRA version:\n%s" % ver)
+    return ver.split("\n", 1)[0]
+
+try:
+    mira_path = os.environ["MIRA4"]
+except KeyError:
+    stop_err("Environment variable $MIRA4 not set")
+mira_binary = os.path.join(mira_path, "mirabait")
+if not os.path.isfile(mira_binary):
+    stop_err("Missing mirabait under $MIRA4, %r\nFolder contained: %s"
+             % (mira_binary, ", ".join(os.listdir(mira_path))))
+mira_ver = get_version(mira_binary)
+if not mira_ver.strip().startswith("4.0"):
+    stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
+    sys.exit(0)
+
+
+format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:]
+
+if format.startswith("fastq"):
+    format = "fastq"
+elif format == "mira":
+    format = "maf"
+elif format != "fasta":
+    stop_err("Was not expected format %r" % format)
+
+assert out_file.endswith(".dat")
+out_file_stem = out_file[:-4]
+
+cmd_list = [mira_binary, "-f", format, "-t", format,
+            "-k", kmer_length, "-n", min_occurance,
+            bait_file, in_file, out_file_stem]
+if output_choice == "pos":
+    pass
+elif output_choice == "neg":
+    #Invert the selection...
+    cmd_list.insert(1, "-i")
+else:
+    stop_err("Output choice should be 'pos' or 'neg', not %r" % output_choice)
+if strand_choice == "both":
+    pass
+elif strand_choice == "fwd":
+    #Ingore reverse strand...
+    cmd_list.insert(1, "-r")
+else:
+    stop_err("Strand choice should be 'both' or 'fwd', not %r" % strand_choice)
+
+cmd = " ".join(cmd_list)
+#print cmd
+start_time = time.time()
+try:
+    #Run MIRA
+    child = subprocess.Popen(cmd_list,
+                             stdout=subprocess.PIPE,
+                             stderr=subprocess.STDOUT)
+except Exception, err:
+    log_manifest(manifest)
+    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()
+assert stderr is None # Due to way we ran with subprocess
+run_time = time.time() - start_time
+return_code = child.returncode
+print "mirabait took %0.2f minutes" % (run_time / 60.0)
+
+if return_code:
+    sys.stderr.write(stdout)
+    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+             return_code)
+
+#Capture output
+out_tmp = out_file_stem + "." + format
+if not os.path.isfile(out_tmp):
+    sys.stderr.write(stdout)
+    stop_err("Missing output file from mirabait: %s" % out_tmp)
+shutil.move(out_tmp, out_file)