| Previous changeset 3:95b13782906c (2012-04-26) |
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Commit message:
Uploaded to the correct location |
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added:
beast.py |
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| diff -r 95b13782906c -r 2ca3df65222b beast.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beast.py Thu Apr 26 11:12:24 2012 -0400 |
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| @@ -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__() |