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author malex
date Thu, 26 Apr 2012 11:12:24 -0400
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3:95b13782906c 4:2ca3df65222b
1 #!/usr/bin/env python
2
3 """
4 Copyright 2012 Oleksandr Moskalenko <om@hpc.ufl.edu>
5
6 Runs BEAST on an input XML file.
7 For use with BEAST version 1.7.1
8
9 usage: beast.py inputxml
10
11 Produces:
12 output log file
13 mcmc.operators file
14 A variable number of '.tree' files depending on the XML input
15 """
16 import os, shutil, subprocess, sys, optparse, glob, string
17 from xml.dom.minidom import parse, Node
18
19 def stop_err(msg):
20 sys.stderr.write("%s\n" % msg)
21 sys.exit()
22
23 def parseFnames(nodelist):
24 filenames = []
25 for node in nodelist:
26 if node.hasAttributes():
27 fname = node.getAttribute('fileName')
28 if fname != "":
29 filenames.append(fname)
30 else:
31 pass
32 return filenames
33
34 def __main__():
35 usage = "usage: %prog inputXML"
36 parser = optparse.OptionParser(usage = usage)
37 parser.add_option("-T", "--threads", action="store", type="string", dest="threads", help="Number of threads")
38 parser.add_option("-s", "--seed", action="store", type="string",
39 dest="seed", help="Random seed")
40 parser.add_option("-r", "--strict", action="store_true", dest="strict", help="Strict XML parsing")
41 parser.add_option("-e", "--errors", action="store", type="string",
42 dest="errors", help="Maximum number of errors allowed")
43 parser.add_option("-i", "--inputxml", action="store", type="string", dest="inputxml", help="Input XML")
44 parser.add_option("-o", "--operators", action="store", type="string", dest="operators", help="Operators")
45 parser.add_option("-l", "--logs", action="store", type="string", dest="logs", help="Logs")
46 parser.add_option("-t", "--trees", action="store", type="string", dest="trees", help="Trees")
47 parser.add_option("-d", "--id", action="store", type="string", dest="treeid", help="Tree ID")
48 parser.add_option("-p", "--path", action="store", type="string", dest="path", help="New file path")
49 (options, args) = parser.parse_args()
50 if options.threads == None:
51 threads = 1
52 else:
53 threads = int(options.threads)
54 if options.seed != None:
55 seed = int(options.seed)
56 else:
57 seed = 12345
58 if options.strict == "-strict":
59 print "Strict XML check was chosen\n"
60 strict = True
61 print "No strict XML check was chosen\n"
62 else:
63 strict = False
64 inputxml = options.inputxml
65 operators = options.operators
66 logs = options.logs
67 trees = options.trees
68 errors = options.errors
69 treefile_id = options.treeid
70 newfilepath = options.path
71 sys.stdout.write("The following parameters have been provided:\n")
72 sys.stdout.write("Input XML: %s\n" % inputxml)
73 sys.stdout.write("Operators: %s\n" % operators)
74 sys.stdout.write("Logs: %s\n" % logs)
75 sys.stdout.write("Trees: %s\n" % trees)
76 sys.stdout.write("Strict: %s\n" % strict)
77 sys.stdout.write("New file path: %s\n" % newfilepath)
78 sys.stdout.write("Tree file ID: %s\n" % treefile_id)
79 if errors != None:
80 sys.stdout.write("Errors: %s\n" % errors)
81 cmd = []
82 cmd.append('beast')
83 if strict == True:
84 cmd.append('-strict')
85 thread_opt = "-threads %d" % threads
86 sys.stdout.write("Threads: %s\n" % thread_opt)
87 cmd.append(thread_opt)
88 cmd.append('-seed %d' % int(seed))
89 if errors != None:
90 cmd.append('-errors %d' % int(errors))
91 cmd.append(inputxml)
92 try:
93 proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
94 except Exception, err:
95 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
96 sys.exit(1)
97 stdout, stderr = proc.communicate()
98 return_code = proc.returncode
99 if return_code:
100 sys.stdout.write(stdout)
101 sys.stderr.write(stderr)
102 sys.stderr.write("Return error code %i from command:\n" % return_code)
103 sys.stderr.write("%s\n" % cmd)
104 sys.exit(1)
105 else:
106 sys.stdout.write(stdout)
107 sys.stdout.write(stderr)
108 #2012-04-24 - 2nd approach, parse the .xml file:
109 xml_file = os.path.abspath(inputxml)
110 if not os.path.exists(inputxml):
111 sys.stderr.write("Cannot find the input XML file for parsing.\n")
112 dom = parse(inputxml)
113 xml_logs = dom.getElementsByTagName('log')
114 xml_trees = dom.getElementsByTagName('logTree')
115 logfiles_orig = parseFnames(xml_logs)
116 treefiles_orig = parseFnames(xml_trees)
117 try:
118 if len(logfiles_orig) == 0:
119 logfiles_orig = glob.glob("*.log*")
120 if len(logfiles_orig) == 0:
121 logfiles_orig.append('Error_no_log')
122 dummy_file = open('Error_no_log','w')
123 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")
124 dummy_file.close()
125 logfiles = []
126 if os.path.isdir(newfilepath):
127 for filename in logfiles_orig:
128 if os.path.isfile(filename):
129 name = string.replace(os.path.splitext(filename)[0], "_", "-")
130 filestring = "primary_%s_%s_visible_nexus" % (treefile_id, name)
131 newpath = os.path.join(newfilepath,filestring)
132 logfiles.append(newpath)
133 # else:
134 # sys.stderr.write("Can't find the log file to rename.\n")
135 logfiles[0] = logs
136 for i in range(len(logfiles_orig)):
137 src = logfiles_orig[i]
138 dst = logfiles[i]
139 if os.path.exists(src):
140 shutil.copy(src, dst)
141 # else:
142 # print "File '%s' can't be found.\n" % src
143 except Exception, err:
144 sys.stderr.write("Error copying log file: \n%s\n" % err)
145 try:
146 if not os.path.exists('mcmc.operators'):
147 bat = open('mcmc.operators','w')
148 bat.write('The mcmc.operators file did not have any output.\n')
149 bat.close()
150 except Exception, err:
151 sys.stderr.write("Error copying mcmc.operators file: \n%s\n" % err)
152 try:
153 if len(treefiles_orig) == 0:
154 print "No tree files found by the xml file parser.\n"
155 treefiles_orig = glob.glob("*.trees*")
156 # print "Original tree files from the directory:\n\t%s" % " ".join(treefiles_orig)
157 if len(treefiles_orig) == 0:
158 treefiles_orig.append('Error_no_tree')
159 dummy_file = open('Error_no_tree','w')
160 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")
161 dummy_file.close()
162 treefiles = []
163 if os.path.isdir(newfilepath):
164 for filename in treefiles_orig:
165 if os.path.isfile(filename):
166 name = string.replace(os.path.splitext(filename)[0], "_", "-")
167 filestring = "primary_%s_%s_visible_nexus" % (treefile_id, name)
168 newpath = os.path.join(newfilepath,filestring)
169 treefiles.append(newpath)
170 treefiles[0] = trees
171 for i in range(len(treefiles_orig)):
172 src = treefiles_orig[i]
173 dst = treefiles[i]
174 if os.path.exists(src):
175 shutil.copy(src, dst)
176 except Exception, err:
177 sys.stderr.write("Error copying trees file(s): \n%s\n" % err)
178 if __name__=="__main__": __main__()