diff tools/sr_assembly/mira.py @ 1:c947750f82fb draft

Uploaded v0.0.5

--- a/tools/sr_assembly/mira.py	Tue Jun 07 15:47:17 2011 -0400
+++ b/tools/sr_assembly/mira.py	Wed Apr 24 11:51:50 2013 -0400
@@ -7,40 +7,57 @@
 import shutil
 import time
 
+WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
+
 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 get_version():
+    """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.
+    try:
+        child = subprocess.Popen(["mira", "-v"],
+                                 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
+    return ver.split("\n", 1)[0]
+
+
+mira_ver = get_version()
+if "V3.4." not in mira_ver:
+    stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
+if "-v" in sys.argv:
+    print "MIRA wrapper version %s," % WRAPPER_VER
+    print mira_ver
+    sys.exit(0)
+
 
 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)]:
+    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
+    if not os.path.isdir(f):
+        stop_err("Missing output folder")
+    if not os.listdir(f):
+        stop_err("Empty output folder")
+    missing = []
+    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
+                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
+                     ("%s/%s_out.wig" % (f, name), out_wig),
+                     ("%s/%s_out.caf" % (f, name), out_caf),
+                     ("%s/%s_out.ace" % (f, name), out_ace)]:
         if not os.path.isfile(old):
-            stop_err("Missing %s output file" % os.path.splitext(old)[-1])
+            missing.append(os.path.splitext(old)[-1])
         else:
             shutil.move(old, new)
+    if missing:
+        stop_err("Missing output files: %s" % ", ".join(missing))
 
 def clean_up(temp, name):
     folder = "%s/%s_assembly" % (temp, name)
@@ -48,22 +65,45 @@
         shutil.rmtree(folder)
 
 #TODO - Run MIRA in /tmp or a configurable directory?
+#Currently Galaxy puts us somewhere safe like:
+#/opt/galaxy-dist/database/job_working_directory/846/
 temp = "."
-name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
+name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
+
 start_time = time.time()
+cmd_list =sys.argv[8:]
+cmd = " ".join(cmd_list)
+
+assert os.path.isdir(temp)
+d = "%s_assembly" % name
+assert not os.path.isdir(d), "Path %s already exists" % d
 try:
-    cmd = " ".join(sys.argv[9:])
-    child = subprocess.Popen(sys.argv[9:],
-                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    #Check path access
+    os.mkdir(d)
+except Exception, err:
+    sys.stderr.write("Error making directory %s\n%s" % (d, err))
+    sys.exit(1)
+
+#print os.path.abspath(".")
+#print cmd
+
+handle = open(out_log, "w")
+try:
+    #Run MIRA
+    child = subprocess.Popen(cmd_list,
+                             stdout=handle,
+                             stderr=subprocess.STDOUT)
 except Exception, err:
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    #TODO - call clean up?
+    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    handle.close()
     sys.exit(1)
 #Use .communicate as can get deadlocks with .wait(),
 stdout, stderr = child.communicate()
+assert not stdout and not stderr #Should be empty as sent to handle
 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:
@@ -75,6 +115,10 @@
              return_code)
 handle.close()
 
+#print "Collecting output..."
 collect_output(temp, name)
+
+#print "Cleaning up..."
 clean_up(temp, name)
+
 print "Done"