--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beast.py	Thu Apr 26 11:12:24 2012 -0400
@@ -0,0 +1,178 @@
+#!/usr/bin/env python
+
+"""
+Copyright 2012 Oleksandr Moskalenko <om@hpc.ufl.edu>
+
+Runs BEAST on an input XML file.
+For use with BEAST version 1.7.1
+
+usage: beast.py inputxml
+
+Produces:
+    output log file
+    mcmc.operators file
+    A variable number of '.tree' files depending on the XML input
+"""
+import os, shutil, subprocess, sys, optparse, glob, string
+from xml.dom.minidom import parse, Node
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def parseFnames(nodelist):
+    filenames = []
+    for node in nodelist:
+        if node.hasAttributes():
+            fname = node.getAttribute('fileName')
+            if fname != "":
+                filenames.append(fname)
+        else:
+            pass
+    return filenames
+
+def __main__():
+    usage = "usage: %prog inputXML"
+    parser = optparse.OptionParser(usage = usage)
+    parser.add_option("-T", "--threads", action="store", type="string", dest="threads", help="Number of threads")
+    parser.add_option("-s", "--seed", action="store", type="string",
+            dest="seed", help="Random seed")
+    parser.add_option("-r", "--strict", action="store_true", dest="strict", help="Strict XML parsing")
+    parser.add_option("-e", "--errors", action="store", type="string",
+            dest="errors", help="Maximum number of errors allowed")
+    parser.add_option("-i", "--inputxml", action="store", type="string", dest="inputxml", help="Input XML") 
+    parser.add_option("-o", "--operators", action="store", type="string", dest="operators", help="Operators")
+    parser.add_option("-l", "--logs", action="store", type="string", dest="logs", help="Logs")
+    parser.add_option("-t", "--trees", action="store", type="string", dest="trees", help="Trees")
+    parser.add_option("-d", "--id", action="store", type="string", dest="treeid", help="Tree ID")
+    parser.add_option("-p", "--path", action="store", type="string", dest="path", help="New file path")
+    (options, args) = parser.parse_args()
+    if options.threads == None:
+        threads = 1
+    else:
+        threads = int(options.threads)
+    if options.seed != None:
+        seed = int(options.seed)
+    else:
+        seed = 12345
+    if options.strict == "-strict":
+        print "Strict XML check was chosen\n"
+        strict = True
+        print "No strict XML check was chosen\n"
+    else:
+        strict = False
+    inputxml = options.inputxml
+    operators = options.operators
+    logs = options.logs
+    trees = options.trees
+    errors = options.errors
+    treefile_id = options.treeid
+    newfilepath = options.path
+    sys.stdout.write("The following parameters have been provided:\n")
+    sys.stdout.write("Input XML: %s\n" % inputxml)
+    sys.stdout.write("Operators: %s\n" % operators)
+    sys.stdout.write("Logs: %s\n" % logs)
+    sys.stdout.write("Trees: %s\n" % trees)
+    sys.stdout.write("Strict: %s\n" % strict)
+    sys.stdout.write("New file path: %s\n" % newfilepath)
+    sys.stdout.write("Tree file ID: %s\n" % treefile_id)
+    if errors != None:
+        sys.stdout.write("Errors: %s\n" % errors)
+    cmd = []
+    cmd.append('beast')
+    if strict == True:
+        cmd.append('-strict')
+    thread_opt = "-threads %d" % threads
+    sys.stdout.write("Threads: %s\n" % thread_opt)
+    cmd.append(thread_opt)
+    cmd.append('-seed %d' % int(seed))
+    if errors != None:
+        cmd.append('-errors %d' % int(errors))
+    cmd.append(inputxml)
+    try:
+        proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
+        sys.exit(1)
+    stdout, stderr = proc.communicate()
+    return_code = proc.returncode
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+        sys.exit(1)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+#2012-04-24 - 2nd approach, parse the .xml file:
+    xml_file = os.path.abspath(inputxml)
+    if not os.path.exists(inputxml):
+        sys.stderr.write("Cannot find the input XML file for parsing.\n")
+    dom = parse(inputxml)
+    xml_logs = dom.getElementsByTagName('log')
+    xml_trees = dom.getElementsByTagName('logTree')
+    logfiles_orig = parseFnames(xml_logs)
+    treefiles_orig = parseFnames(xml_trees)
+    try:
+        if len(logfiles_orig) == 0:
+            logfiles_orig = glob.glob("*.log*")
+            if len(logfiles_orig) == 0:
+                logfiles_orig.append('Error_no_log')
+                dummy_file = open('Error_no_log','w')
+                dummy_file.write("BEAST run has not produced a log or it's named in such a way that I can't locate it. Configure BEAST to produce .log files without spaces in their names and rerun the analysis.\n")
+                dummy_file.close()
+        logfiles = []
+        if os.path.isdir(newfilepath):
+            for filename in logfiles_orig:
+                if os.path.isfile(filename):
+                    name = string.replace(os.path.splitext(filename)[0], "_", "-")
+                    filestring = "primary_%s_%s_visible_nexus" % (treefile_id, name)
+                    newpath = os.path.join(newfilepath,filestring)
+                    logfiles.append(newpath)
+#                else:
+#                    sys.stderr.write("Can't find the log file to rename.\n")
+        logfiles[0] = logs
+        for i in range(len(logfiles_orig)):
+            src = logfiles_orig[i]
+            dst = logfiles[i]
+            if os.path.exists(src):
+                shutil.copy(src, dst)
+#            else:
+#                print "File '%s' can't be found.\n" % src
+    except Exception, err:
+        sys.stderr.write("Error copying log file: \n%s\n" % err)
+    try:
+        if not os.path.exists('mcmc.operators'):
+            bat = open('mcmc.operators','w')
+            bat.write('The mcmc.operators file did not have any output.\n')
+            bat.close()
+    except Exception, err:
+        sys.stderr.write("Error copying mcmc.operators file: \n%s\n" % err)
+    try:
+        if len(treefiles_orig) == 0:
+            print "No tree files found by the xml file parser.\n"
+            treefiles_orig = glob.glob("*.trees*")
+#                print "Original tree files from the directory:\n\t%s" % " ".join(treefiles_orig)
+            if len(treefiles_orig) == 0:
+                treefiles_orig.append('Error_no_tree')
+                dummy_file = open('Error_no_tree','w')
+                dummy_file.write("BEAST run has not produced an output tree or it's named in such a way that I can't locate it. Configure BEAST to produce .tree files without spaces in their names and rerun the analysis.\n")
+                dummy_file.close()
+        treefiles = []
+        if os.path.isdir(newfilepath):
+            for filename in treefiles_orig:
+                if os.path.isfile(filename):
+                    name = string.replace(os.path.splitext(filename)[0], "_", "-")
+                    filestring = "primary_%s_%s_visible_nexus" % (treefile_id, name)
+                    newpath = os.path.join(newfilepath,filestring)
+                    treefiles.append(newpath)
+        treefiles[0] = trees
+        for i in range(len(treefiles_orig)):
+            src = treefiles_orig[i]
+            dst = treefiles[i]
+            if os.path.exists(src):
+                shutil.copy(src, dst)
+    except Exception, err:
+        sys.stderr.write("Error copying trees file(s): \n%s\n" % err)
+if __name__=="__main__": __main__()