--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4_0/mira4.py	Wed Sep 02 07:46:29 2015 -0400
@@ -0,0 +1,313 @@
+#!/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
+import tempfile
+from optparse import OptionParser
+
+#Do we need any PYTHONPATH magic?
+from mira4_make_bam import make_bam
+
+WRAPPER_VER = "0.0.4" #Keep in sync with the XML file
+
+def sys_exit(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
+    return ver.split("\n", 1)[0].strip()
+
+#Parse Command Line
+usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
+
+$ python mira4.py ...
+
+This will run the MIRA binary and collect its output files as directed.
+""" % WRAPPER_VER
+parser = OptionParser(usage=usage)
+parser.add_option("-m", "--manifest", dest="manifest",
+                  default=None, metavar="FILE",
+                  help="MIRA manifest filename")
+parser.add_option("--maf", dest="maf",
+                  default="-", metavar="FILE",
+                  help="MIRA MAF output filename")
+parser.add_option("--bam", dest="bam",
+                  default="-", metavar="FILE",
+                  help="Unpadded BAM output filename")
+parser.add_option("--fasta", dest="fasta",
+                  default="-", metavar="FILE",
+                  help="Unpadded FASTA output filename")
+parser.add_option("--log", dest="log",
+                  default="-", metavar="FILE",
+                  help="MIRA logging output filename")
+parser.add_option("-v", "--version", dest="version",
+                  default=False, action="store_true",
+                  help="Show version and quit")
+options, args = parser.parse_args()
+manifest = options.manifest
+out_maf = options.maf
+out_bam = options.bam
+out_fasta = options.fasta
+out_log = options.log
+
+try:
+    mira_path = os.environ["MIRA4"]
+except KeyError:
+    sys_exit("Environment variable $MIRA4 not set")
+mira_binary = os.path.join(mira_path, "mira")
+if not os.path.isfile(mira_binary):
+    sys_exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
+             % (mira_binary, ", ".join(os.listdir(mira_path))))
+mira_convert = os.path.join(mira_path, "miraconvert")
+if not os.path.isfile(mira_convert):
+    sys_exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
+             % (mira_convert, ", ".join(os.listdir(mira_path))))
+
+mira_ver = get_version(mira_binary)
+if not mira_ver.strip().startswith("4.0"):
+    sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_binary))
+mira_convert_ver = get_version(mira_convert)
+if not mira_convert_ver.strip().startswith("4.0"):
+    sys_exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_ver, mira_convert))
+if options.version:
+    print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_VER)
+    if mira_ver != mira_convert_ver:
+        print "WARNING: miraconvert %s" % mira_convert_ver
+    sys.exit(0)
+
+if not manifest:
+    sys_exit("Manifest is required")
+elif not os.path.isfile(manifest):
+    sys_exit("Missing input MIRA manifest file: %r" % manifest)
+
+
+try:
+    threads = int(os.environ.get("GALAXY_SLOTS", "1"))
+except ValueError:
+    threads = 1
+assert 1 <= threads, threads
+
+
+def override_temp(manifest):
+    """Override ``-DI:trt=/tmp`` in manifest with environment variable.
+
+    Currently MIRA 4 does not allow envronment variables like ``$TMP``
+    inside the manifest, which is a problem if you need to override
+    the default at run time.
+
+    The tool XML will ``/tmp`` and we replace that here with
+    ``tempfile.gettempdir()`` which will respect $TMPDIR, $TEMP, $TMP
+    as explained in the Python standard library documentation:
+    http://docs.python.org/2/library/tempfile.html#tempfile.tempdir
+
+    By default MIRA 4 would write its temporary files within the output
+    folder, which is a problem if that is a network drive.
+    """
+    handle = open(manifest, "r")
+    text = handle.read()
+    handle.close()
+
+    #At time of writing, this is at the end of a file,
+    #but could be followed by a space in future...
+    text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
+
+    #Want to try to ensure this gets written to disk before MIRA attempts
+    #to open it - any networked file system may impose a delay...
+    handle = open(manifest, "w")
+    handle.write(text)
+    handle.flush()
+    os.fsync(handle.fileno())
+    handle.close()
+
+
+def log_manifest(manifest):
+    """Write the manifest file to stderr."""
+    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
+    with open(manifest) as h:
+        for line in h:
+            sys.stderr.write(line)
+    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
+
+
+def collect_output(temp, name, handle):
+    """Moves files to the output filenames (global variables)."""
+    n3 = (temp, name, name, name)
+    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
+    if not os.path.isdir(f):
+        log_manifest(manifest)
+        sys_exit("Missing output folder")
+    if not os.listdir(f):
+        log_manifest(manifest)
+        sys_exit("Empty output folder")
+    missing = []
+
+    old_maf = "%s/%s_out.maf" % (f, name)
+    if not os.path.isfile(old_maf):
+        #Triggered extractLargeContigs.sh?
+        old_maf = "%s/%s_LargeContigs_out.maf" % (f, name)
+
+    #De novo or single strain mapping,
+    old_fasta = "%s/%s_out.unpadded.fasta" % (f, name)
+    ref_fasta = "%s/%s_out.padded.fasta" % (f, name)
+    if not os.path.isfile(old_fasta):
+        #Mapping (StrainX versus reference) or de novo
+        old_fasta = "%s/%s_out_StrainX.unpadded.fasta" % (f, name)
+        ref_fasta = "%s/%s_out_StrainX.padded.fasta" % (f, name)
+    if not os.path.isfile(old_fasta):
+        old_fasta = "%s/%s_out_ReferenceStrain.unpadded.fasta" % (f, name)
+        ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
+        
+
+    missing = False
+    for old, new in [(old_maf, out_maf),
+                     (old_fasta, out_fasta)]:
+        if not os.path.isfile(old):
+            missing = True
+        elif not new or new == "-":
+            handle.write("Ignoring %s\n" % old)
+        else:
+            handle.write("Capturing %s\n" % old)
+            shutil.move(old, new)
+    if missing:
+        log_manifest(manifest)
+        sys.stderr.write("Contents of %r:\n" % f)
+        for filename in sorted(os.listdir(f)):
+            sys.stderr.write("%s\n" % filename)
+
+    #For mapping mode, probably most people would expect a BAM file
+    #using the reference FASTA file...
+    if out_bam and out_bam != "-":
+        if out_maf and out_maf != "-":
+            msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
+        else:
+            #Not collecting the MAF file, use original location        
+            msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
+        if msg:
+            sys_exit(msg)
+
+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?
+#Currently Galaxy puts us somewhere safe like:
+#/opt/galaxy-dist/database/job_working_directory/846/
+temp = "."
+
+name = "MIRA"
+
+override_temp(manifest)
+
+start_time = time.time()
+cmd_list = [mira_binary, "-t", str(threads), manifest]
+cmd = " ".join(cmd_list)
+
+assert os.path.isdir(temp)
+d = "%s_assembly" % name
+#This can fail on my development machine if stale folders exist
+#under Galaxy's .../database/job_working_directory/ tree:
+assert not os.path.isdir(d), "Path %r already exists:\n%s" % (d, os.path.abspath(d))
+try:
+    #Check path access
+    os.mkdir(d)
+except Exception, err:
+    log_manifest(manifest)
+    sys.stderr.write("Error making directory %s\n%s" % (d, err))
+    sys.exit(1)
+
+#print os.path.abspath(".")
+#print cmd
+
+if out_log and out_log != "-":
+    handle = open(out_log, "w")
+else:
+    handle = open(os.devnull, "w")
+handle.write("======================== MIRA manifest (instructions) ========================\n")
+m = open(manifest, "rU")
+for line in m:
+    handle.write(line)
+m.close()
+del m
+handle.write("\n")
+handle.write("============================ Starting MIRA now ===============================\n")
+handle.flush()
+try:
+    #Run MIRA
+    child = subprocess.Popen(cmd_list,
+                             stdout=handle,
+                             stderr=subprocess.STDOUT)
+except Exception, err:
+    log_manifest(manifest)
+    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.write("\n")
+handle.write("============================ MIRA has finished ===============================\n")
+handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
+if return_code:
+    print "MIRA took %0.2f hours" % (run_time / 3600.0)
+    handle.write("Return error code %i from command:\n" % return_code)
+    handle.write(cmd + "\n")
+    handle.close()
+    clean_up(temp, name)
+    log_manifest(manifest)
+    sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
+             return_code)
+handle.flush()
+
+if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
+    handle.write("\n")
+    handle.write("====================== Extract Large Contigs failed ==========================\n")
+    e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
+    for line in e:
+        handle.write(line)
+    e.close()
+    handle.write("============================ (end of ec.log) =================================\n")
+    handle.flush()
+
+#print "Collecting output..."
+start_time = time.time()
+collect_output(temp, name, handle)
+collect_time = time.time() - start_time
+handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
+print("MIRA took %0.2f hours; collecting output %0.2f minutes\n" % (run_time / 3600.0, collect_time / 60.0))
+
+if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
+    #Treat as an error, but doing this AFTER collect_output
+    sys.stderr.write("Extract Large Contigs failed\n")
+    handle.write("Extract Large Contigs failed\n")
+    handle.close()
+    sys.exit(1)
+
+#print "Cleaning up..."
+clean_up(temp, name)
+
+handle.write("\nDone\n")
+handle.close()
+print("Done")