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Uploaded the first beta.
author malex
date Tue, 02 Oct 2012 17:35:46 -0400
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-1:000000000000 0:d95d87f40f47
1 #!/usr/bin/env python
2 """
3 Runs RAxML on a sequence file.
4 For use with RAxML version 7.3.0
5
6 usage:
7 <!-- raxmlHPC-PTHREADS-SSE3 -T 2 -f c -m GTRGAMMA -F -s "/Users/om/Downloads/rana.phy" -n rana_red -w "/Users/om/Downloads/" 0
8 ## raxmlHPC-PTHREADS-SSE3 -T 2 -m GTRGAMMA -n test -p 323483 -s reduced.phy
9 command>raxmlHPC-HYBRID-SSE3 -T 4 -f ${search_algorithm} -m ${smodel} -N ${repeats} -o "${html_outfile.files_path}" -s "$input1"
10 """
11 import os, shutil, subprocess, sys, optparse, fnmatch, glob
12
13 def stop_err(msg):
14 sys.stderr.write("%s\n" % msg)
15 sys.exit()
16
17 def getint(name):
18 basename = name.partition('RUN.')
19 if basename[2] != '':
20 num = basename[2]
21 return int(num)
22
23 def __main__():
24 usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]"
25
26 # Parse the primary wrapper's command line options
27 parser = optparse.OptionParser(usage = usage)
28 # raxml binary name, hardcoded in the xml file
29 parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run")
30 # (-a)
31 parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file")
32 # (-A)
33 parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model")
34 # (-b)
35 parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed")
36 # (-c)
37 parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories")
38 # (-d)
39 parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree")
40 # (-D)
41 parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion")
42 # (-e)
43 parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)")
44 # (-E)
45 parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name")
46 # (-f)
47 parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm")
48 # (-F)
49 parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models")
50 # (-g)
51 parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name")
52 # (-G)
53 parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics")
54 # (-i)
55 parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting")
56 # (-I)
57 parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis")
58 # (-J)
59 parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus")
60 # (-k)
61 parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths")
62 # (-K)
63 parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model")
64 # (-m)
65 parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type")
66 parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model")
67 parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences")
68 parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix")
69 # (-n)
70 parser.add_option("--name", action="store", type="string", dest="name", help="Run Name")
71 # (-N/#)
72 parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", help="Number of alternative runs")
73 parser.add_option("--number_of_runs_bootstop", action="store", type="string", dest="number_of_runs_bootstop", help="Number of alternative runs based on the bootstop criteria")
74 # (-M)
75 parser.add_option("--estimate_individual_branch_lengths", action="store_true", dest="estimate_individual_branch_lengths", help="Estimate individual branch lengths")
76 # (-o)
77 parser.add_option("--outgroup_name", action="store", type="string", dest="outgroup_name", help="Outgroup Name")
78 # (-O)
79 parser.add_option("--disable_undetermined_seq_check", action="store_true", dest="disable_undetermined_seq_check", help="Disable undetermined sequence check")
80 # (-p)
81 parser.add_option("--random_seed", action="store", type="int", dest="random_seed", help="Random Number Seed")
82 # (-P)
83 parser.add_option("--external_protein_model", action="store", type="string", dest="external_protein_model", help="External Protein Model")
84 # (-q)
85 parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File")
86 # (-r)
87 parser.add_option("--constraint_file", action="store", type="string", dest="constraint_file", help="Constraint File")
88 # (-R)
89 parser.add_option("--bin_model_parameter_file", action="store", type="string", dest="bin_model_parameter_file", help="Constraint File")
90 # (-s)
91 parser.add_option("--source", action="store", type="string", dest="source", help="Input file")
92 # (-S)
93 parser.add_option("--secondary_structure_file", action="store", type="string", dest="secondary_structure_file", help="Secondary structure file")
94 # (-t)
95 parser.add_option("--starting_tree", action="store", type="string", dest="starting_tree", help="Starting Tree")
96 # (-T)
97 parser.add_option("--threads", action="store", type="int", dest="threads", help="Number of threads to use")
98 # (-u)
99 parser.add_option("--use_median_approximation", action="store_true", dest="use_median_approximation", help="Use median approximation")
100 # (-U)
101 parser.add_option("--save_memory_gappy_alignments", action="store_true", dest="save_memory_gappy_alignments", help="Save memory in large gapped alignments")
102 # (-V)
103 parser.add_option("--disable_rate_heterogeneity", action="store_true", dest="disable_rate_heterogeneity", help="Disable rate heterogeneity")
104 # (-W)
105 parser.add_option("--sliding_window_size", action="store", type="string", dest="sliding_window_size", help="Sliding window size")
106 # (-x)
107 parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed")
108 # (-y)
109 parser.add_option("--parsimony_starting_tree_only", action="store_true", dest="parsimony_starting_tree_only", help="Generate a parsimony starting tree only")
110 # (-z)
111 parser.add_option("--file_multiple_trees", action="store", type="string", dest="file_multiple_trees", help="Multiple Trees File")
112
113 (options, args) = parser.parse_args()
114 cmd = []
115
116 # Required parameters
117 binary = options.binary
118 cmd.append(binary)
119 # Threads
120 threads = "-T %d" % options.threads
121 cmd.append(threads)
122 # Source
123 source = "-s %s" % options.source
124 cmd.append(source)
125 #Hardcode to "galaxy" first to simplify the output part of the wrapper
126 #name = "-n %s" % options.name
127 name = "-n galaxy"
128 cmd.append(name)
129 ## Model
130 model_type = options.model_type
131 base_model = options.base_model
132 aa_search_matrix = options.aa_search_matrix
133 aa_empirical_freq = options.aa_empirical_freq
134 if model_type == 'aminoacid':
135 model = "-m %s%s" % (base_model, aa_search_matrix)
136 if aa_empirical_freq:
137 model = "-m %s%s%s" % (base_model, aa_search_matrix, 'F')
138 # (-P)
139 if options.external_protein_model:
140 external_protein_model = "-P %s" % options.external_protein_model
141 cmd.append(external_protein_model)
142 else:
143 model = "-m %s" % base_model
144 cmd.append(model)
145 if model == "GTRCAT":
146 # (-c)
147 if options.numofcats:
148 numofcats = "-c %d" % options.numofcats
149 cmd.append(numofcats)
150 # Optional parameters
151 if options.number_of_runs_bootstop:
152 number_of_runs_bootstop = "-N %s" % options.number_of_runs_bootstop
153 cmd.append(number_of_runs_bootstop)
154 else:
155 number_of_runs_bootstop = ''
156 if options.number_of_runs:
157 number_of_runs_opt = "-N %d" % options.number_of_runs
158 cmd.append(number_of_runs_opt)
159 else:
160 number_of_runs_opt = 0
161 # (-a)
162 if options.weightfile:
163 weightfile = "-a %s" % options.weightfile
164 cmd.append(weightfile)
165 # (-A)
166 if options.secondary_structure_model:
167 secondary_structure_model = "-A %s" % options.secondary_structure_model
168 cmd.append(secondary_structure_model )
169 # (-b)
170 if options.bootseed:
171 bootseed = "-b %d" % options.bootseed
172 cmd.append(bootseed)
173 else:
174 bootseed = 0
175 # -C - doesn't work in pthreads version, skipped
176 if options.search_complete_random_tree:
177 cmd.append("-d")
178 if options.ml_search_convergence:
179 cmd.append("-D" )
180 if options.model_opt_precision:
181 model_opt_precision = "-e %f" % options.model_opt_precision
182 cmd.append(model_opt_precision)
183 if options.excludefile:
184 excludefile = "-E %s" % options.excludefile
185 cmd.append(excludefile)
186 if options.search_algorithm:
187 search_algorithm = "-f %s" % options.search_algorithm
188 cmd.append(search_algorithm)
189 if options.save_memory_cat_model:
190 cmd.append("-F")
191 if options.groupingfile:
192 groupingfile = "-g %s" % options.groupingfile
193 cmd.append(groupingfile)
194 if options.enable_evol_heuristics:
195 enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics
196 cmd.append(enable_evol_heuristics )
197 if options.initial_rearrangement_setting:
198 initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting
199 cmd.append(initial_rearrangement_setting)
200 if options.posterior_bootstopping_analysis:
201 posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis
202 cmd.append(posterior_bootstopping_analysis)
203 if options.majority_rule_consensus:
204 majority_rule_consensus = "-J %s" % options.majority_rule_consensus
205 cmd.append(majority_rule_consensus)
206 if options.print_branch_lengths:
207 cmd.append("-k")
208 if options.multistate_sub_model:
209 multistate_sub_model = "-K %s" % options.multistate_sub_model
210 cmd.append(multistate_sub_model)
211 if options.estimate_individual_branch_lengths:
212 cmd.append("-M")
213 if options.outgroup_name:
214 outgroup_name = "-o %s" % options.outgroup_name
215 cmd.append(outgroup_name)
216 if options.disable_undetermined_seq_check:
217 cmd.append("-O")
218 if options.random_seed:
219 random_seed = "-p %d" % options.random_seed
220 cmd.append(random_seed)
221 multiple_model = None
222 if options.multiple_model:
223 multiple_model = "-q %s" % options.multiple_model
224 cmd.append(multiple_model)
225 if options.constraint_file:
226 constraint_file = "-r %s" % options.constraint_file
227 cmd.append(constraint_file)
228 if options.bin_model_parameter_file:
229 bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy"
230 os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name )
231 bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file
232 #Needs testing. Is the hardcoded name or the real path needed?
233 cmd.append(bin_model_parameter_file)
234 if options.secondary_structure_file:
235 secondary_structure_file = "-S %s" % options.secondary_structure_file
236 cmd.append(secondary_structure_file)
237 if options.starting_tree:
238 starting_tree = "-t %s" % options.starting_tree
239 cmd.append(starting_tree)
240 if options.use_median_approximation:
241 cmd.append("-u")
242 if options.save_memory_gappy_alignments:
243 cmd.append("-U")
244 if options.disable_rate_heterogeneity:
245 cmd.append("-V")
246 if options.sliding_window_size:
247 sliding_window_size = "-W %d" % options.sliding_window_size
248 cmd.append(sliding_window_size)
249 if options.rapid_bootstrap_random_seed:
250 rapid_bootstrap_random_seed = "-x %d" % options.rapid_bootstrap_random_seed
251 cmd.append(rapid_bootstrap_random_seed)
252 else:
253 rapid_bootstrap_random_seed = 0
254 if options.parsimony_starting_tree_only:
255 cmd.append("-y")
256 if options.file_multiple_trees:
257 file_multiple_trees = "-z %s" % options.file_multiple_trees
258 cmd.append(file_multiple_trees)
259
260 print "cmd list: ", cmd, "\n"
261
262 full_cmd = " ".join(cmd)
263 print "Command string: %s" % full_cmd
264
265 try:
266 proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
267 except Exception, err:
268 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
269 sys.exit(1)
270 stdout, stderr = proc.communicate()
271 return_code = proc.returncode
272 if return_code:
273 sys.stdout.write(stdout)
274 sys.stderr.write(stderr)
275 sys.stderr.write("Return error code %i from command:\n" % return_code)
276 sys.stderr.write("%s\n" % cmd)
277 else:
278 sys.stdout.write(stdout)
279 sys.stdout.write(stderr)
280
281 #Multiple runs - concatenate
282 if number_of_runs_opt > 0:
283 if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ):
284 runfiles = glob.glob('RAxML*RUN*')
285 runfiles.sort(key=getint)
286 # Logs
287 outfile = open('RAxML_log.galaxy','w')
288 for filename in runfiles:
289 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'):
290 infile = open(filename, 'r')
291 filename_line = "%s\n" % filename
292 outfile.write(filename_line)
293 for line in infile:
294 outfile.write(line)
295 infile.close()
296 outfile.close()
297 # Parsimony Trees
298 outfile = open('RAxML_parsimonyTree.galaxy','w')
299 for filename in runfiles:
300 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'):
301 infile = open(filename, 'r')
302 filename_line = "%s\n" % filename
303 outfile.write(filename_line)
304 for line in infile:
305 outfile.write(line)
306 infile.close()
307 outfile.close()
308 # Results
309 outfile = open('RAxML_result.galaxy','w')
310 for filename in runfiles:
311 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'):
312 infile = open(filename, 'r')
313 filename_line = "%s\n" % filename
314 outfile.write(filename_line)
315 for line in infile:
316 outfile.write(line)
317 infile.close()
318 outfile.close()
319 # Multiple Model Partition Files
320 if multiple_model:
321 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*')
322 if len(files) > 0:
323 files.sort(key=getint)
324 outfile = open('RAxML_bestTreePartitions.galaxy','w')
325 # Best Tree Partitions
326 for filename in files:
327 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'):
328 infile = open(filename, 'r')
329 filename_line = "%s\n" % filename
330 outfile.write(filename_line)
331 for line in infile:
332 outfile.write(line)
333 infile.close()
334 outfile.close()
335 else:
336 outfile = open('RAxML_bestTreePartitions.galaxy','w')
337 outfile.write("No partition files were produced.\n")
338 outfile.close()
339
340 # Result Partitions
341 files = glob.glob('RAxML_result.galaxy.PARTITION.*')
342 if len(files) > 0:
343 files.sort(key=getint)
344 outfile = open('RAxML_resultPartitions.galaxy','w')
345 for filename in files:
346 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'):
347 infile = open(filename, 'r')
348 filename_line = "%s\n" % filename
349 outfile.write(filename_line)
350 for line in infile:
351 outfile.write(line)
352 infile.close()
353 outfile.close()
354 else:
355 outfile = open('RAxML_resultPartitions.galaxy','w')
356 outfile.write("No partition files were produced.\n")
357 outfile.close()
358
359 # DEBUG options
360 infof = open('RAxML_info.galaxy','a')
361 infof.write('\nOM: CLI options DEBUG START:\n')
362 infof.write(options.__repr__())
363 infof.write('\nOM: CLI options DEBUG END\n')
364
365 if __name__=="__main__": __main__()