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comparison raxml.py @ 1:b0d6eb76ad87 draft

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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 80c5ab90ac30fe083328ef7ad507d2e578daea90
author iuc
date Sat, 25 Jun 2016 19:34:35 -0400
parents 934206441123
children 6f7ff8a3bd79
comparison
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0:934206441123 1:b0d6eb76ad87
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 """ 2 """
3 Runs RAxML on a sequence file. 3 Runs RAxML on a sequence file.
4 For use with RAxML version 8.2.4 4 For use with RAxML version 8.2.4
5 """ 5 """
6 import os, shutil, subprocess, sys, optparse, fnmatch, glob 6 import fnmatch
7 import glob
8 import optparse
9 import os
10 import subprocess
11 import sys
12
7 13
8 def stop_err(msg): 14 def stop_err(msg):
9 sys.stderr.write("%s\n" % msg) 15 sys.stderr.write("%s\n" % msg)
10 sys.exit() 16 sys.exit()
17
11 18
12 def getint(name): 19 def getint(name):
13 basename = name.partition('RUN.') 20 basename = name.partition('RUN.')
14 if basename[2] != '': 21 if basename[2] != '':
15 num = basename[2] 22 num = basename[2]
16 return int(num) 23 return int(num)
17 24
25
18 def __main__(): 26 def __main__():
19 usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]" 27 usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]"
20 28
21 # Parse the primary wrapper's command line options 29 # Parse the primary wrapper's command line options
22 parser = optparse.OptionParser(usage = usage) 30 parser = optparse.OptionParser(usage=usage)
23 # raxml binary name, hardcoded in the xml file 31 # raxml binary name, hardcoded in the xml file
24 parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run") 32 parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run")
25 # (-a) 33 # (-a)
26 parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file") 34 parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file")
27 # (-A) 35 # (-A)
116 threads = "-T %d" % options.threads 124 threads = "-T %d" % options.threads
117 cmd.append(threads) 125 cmd.append(threads)
118 # Source 126 # Source
119 source = "-s %s" % options.source 127 source = "-s %s" % options.source
120 cmd.append(source) 128 cmd.append(source)
121 #Hardcode to "galaxy" first to simplify the output part of the wrapper 129 # Hardcode to "galaxy" first to simplify the output part of the wrapper
122 #name = "-n %s" % options.name 130 # name = "-n %s" % options.name
123 name = "-n galaxy" 131 name = "-n galaxy"
124 cmd.append(name) 132 cmd.append(name)
125 ## Model 133 # Model
126 model_type = options.model_type 134 model_type = options.model_type
127 base_model = options.base_model 135 base_model = options.base_model
128 aa_search_matrix = options.aa_search_matrix 136 aa_search_matrix = options.aa_search_matrix
129 aa_empirical_freq = options.aa_empirical_freq 137 aa_empirical_freq = options.aa_empirical_freq
130 if model_type == 'aminoacid': 138 if model_type == 'aminoacid':
158 if options.weightfile: 166 if options.weightfile:
159 weightfile = "-a %s" % options.weightfile 167 weightfile = "-a %s" % options.weightfile
160 cmd.append(weightfile) 168 cmd.append(weightfile)
161 # (-A) 169 # (-A)
162 if options.secondary_structure_model: 170 if options.secondary_structure_model:
163 secondary_structure_model = "-A %s" % options.secondary_structure_model 171 secondary_structure_model = "-A %s" % options.secondary_structure_model
164 cmd.append(secondary_structure_model ) 172 cmd.append(secondary_structure_model )
165 # (-b) 173 # (-b)
166 if options.bootseed: 174 if options.bootseed:
167 bootseed = "-b %d" % options.bootseed 175 bootseed = "-b %d" % options.bootseed
168 cmd.append(bootseed) 176 cmd.append(bootseed)
189 cmd.append(groupingfile) 197 cmd.append(groupingfile)
190 if options.enable_evol_heuristics: 198 if options.enable_evol_heuristics:
191 enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics 199 enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics
192 cmd.append(enable_evol_heuristics ) 200 cmd.append(enable_evol_heuristics )
193 if options.initial_rearrangement_setting: 201 if options.initial_rearrangement_setting:
194 initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting 202 initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting
195 cmd.append(initial_rearrangement_setting) 203 cmd.append(initial_rearrangement_setting)
196 if options.posterior_bootstopping_analysis: 204 if options.posterior_bootstopping_analysis:
197 posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis 205 posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis
198 cmd.append(posterior_bootstopping_analysis) 206 cmd.append(posterior_bootstopping_analysis)
199 if options.majority_rule_consensus: 207 if options.majority_rule_consensus:
223 cmd.append(constraint_file) 231 cmd.append(constraint_file)
224 if options.bin_model_parameter_file: 232 if options.bin_model_parameter_file:
225 bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy" 233 bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy"
226 os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name ) 234 os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name )
227 bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file 235 bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file
228 #Needs testing. Is the hardcoded name or the real path needed? 236 # Needs testing. Is the hardcoded name or the real path needed?
229 cmd.append(bin_model_parameter_file) 237 cmd.append(bin_model_parameter_file)
230 if options.secondary_structure_file: 238 if options.secondary_structure_file:
231 secondary_structure_file = "-S %s" % options.secondary_structure_file 239 secondary_structure_file = "-S %s" % options.secondary_structure_file
232 cmd.append(secondary_structure_file) 240 cmd.append(secondary_structure_file)
233 if options.starting_tree: 241 if options.starting_tree:
258 full_cmd = " ".join(cmd) 266 full_cmd = " ".join(cmd)
259 print "Command string: %s" % full_cmd 267 print "Command string: %s" % full_cmd
260 268
261 try: 269 try:
262 proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 270 proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
263 except Exception, err: 271 except Exception as err:
264 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err)) 272 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
265 sys.exit(1) 273 sys.exit(1)
266 stdout, stderr = proc.communicate() 274 stdout, stderr = proc.communicate()
267 return_code = proc.returncode 275 return_code = proc.returncode
268 if return_code: 276 if return_code:
272 sys.stderr.write("%s\n" % cmd) 280 sys.stderr.write("%s\n" % cmd)
273 else: 281 else:
274 sys.stdout.write(stdout) 282 sys.stdout.write(stdout)
275 sys.stdout.write(stderr) 283 sys.stdout.write(stderr)
276 284
277 #Multiple runs - concatenate 285 # Multiple runs - concatenate
278 if number_of_runs_opt > 0: 286 if number_of_runs_opt > 0:
279 if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ): 287 if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ):
280 runfiles = glob.glob('RAxML*RUN*') 288 runfiles = glob.glob('RAxML*RUN*')
281 runfiles.sort(key=getint) 289 runfiles.sort(key=getint)
282 # Logs 290 # Logs
283 outfile = open('RAxML_log.galaxy','w') 291 outfile = open('RAxML_log.galaxy', 'w')
284 for filename in runfiles: 292 for filename in runfiles:
285 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): 293 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'):
286 infile = open(filename, 'r') 294 infile = open(filename, 'r')
287 filename_line = "%s\n" % filename 295 filename_line = "%s\n" % filename
288 outfile.write(filename_line) 296 outfile.write(filename_line)
289 for line in infile: 297 for line in infile:
290 outfile.write(line) 298 outfile.write(line)
291 infile.close() 299 infile.close()
292 outfile.close() 300 outfile.close()
293 # Parsimony Trees 301 # Parsimony Trees
294 outfile = open('RAxML_parsimonyTree.galaxy','w') 302 outfile = open('RAxML_parsimonyTree.galaxy', 'w')
295 for filename in runfiles: 303 for filename in runfiles:
296 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): 304 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'):
297 infile = open(filename, 'r') 305 infile = open(filename, 'r')
298 filename_line = "%s\n" % filename 306 filename_line = "%s\n" % filename
299 outfile.write(filename_line) 307 outfile.write(filename_line)
300 for line in infile: 308 for line in infile:
301 outfile.write(line) 309 outfile.write(line)
302 infile.close() 310 infile.close()
303 outfile.close() 311 outfile.close()
304 # Results 312 # Results
305 outfile = open('RAxML_result.galaxy','w') 313 outfile = open('RAxML_result.galaxy', 'w')
306 for filename in runfiles: 314 for filename in runfiles:
307 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): 315 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'):
308 infile = open(filename, 'r') 316 infile = open(filename, 'r')
309 filename_line = "%s\n" % filename 317 filename_line = "%s\n" % filename
310 outfile.write(filename_line) 318 outfile.write(filename_line)
315 # Multiple Model Partition Files 323 # Multiple Model Partition Files
316 if multiple_model: 324 if multiple_model:
317 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*') 325 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*')
318 if len(files) > 0: 326 if len(files) > 0:
319 files.sort(key=getint) 327 files.sort(key=getint)
320 outfile = open('RAxML_bestTreePartitions.galaxy','w') 328 outfile = open('RAxML_bestTreePartitions.galaxy', 'w')
321 # Best Tree Partitions 329 # Best Tree Partitions
322 for filename in files: 330 for filename in files:
323 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): 331 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'):
324 infile = open(filename, 'r') 332 infile = open(filename, 'r')
325 filename_line = "%s\n" % filename 333 filename_line = "%s\n" % filename
327 for line in infile: 335 for line in infile:
328 outfile.write(line) 336 outfile.write(line)
329 infile.close() 337 infile.close()
330 outfile.close() 338 outfile.close()
331 else: 339 else:
332 outfile = open('RAxML_bestTreePartitions.galaxy','w') 340 outfile = open('RAxML_bestTreePartitions.galaxy', 'w')
333 outfile.write("No partition files were produced.\n") 341 outfile.write("No partition files were produced.\n")
334 outfile.close() 342 outfile.close()
335 343
336 # Result Partitions 344 # Result Partitions
337 files = glob.glob('RAxML_result.galaxy.PARTITION.*') 345 files = glob.glob('RAxML_result.galaxy.PARTITION.*')
338 if len(files) > 0: 346 if len(files) > 0:
339 files.sort(key=getint) 347 files.sort(key=getint)
340 outfile = open('RAxML_resultPartitions.galaxy','w') 348 outfile = open('RAxML_resultPartitions.galaxy', 'w')
341 for filename in files: 349 for filename in files:
342 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): 350 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'):
343 infile = open(filename, 'r') 351 infile = open(filename, 'r')
344 filename_line = "%s\n" % filename 352 filename_line = "%s\n" % filename
345 outfile.write(filename_line) 353 outfile.write(filename_line)
346 for line in infile: 354 for line in infile:
347 outfile.write(line) 355 outfile.write(line)
348 infile.close() 356 infile.close()
349 outfile.close() 357 outfile.close()
350 else: 358 else:
351 outfile = open('RAxML_resultPartitions.galaxy','w') 359 outfile = open('RAxML_resultPartitions.galaxy', 'w')
352 outfile.write("No partition files were produced.\n") 360 outfile.write("No partition files were produced.\n")
353 outfile.close() 361 outfile.close()
354 362
355 # DEBUG options 363 # DEBUG options
356 infof = open('RAxML_info.galaxy','a') 364 infof = open('RAxML_info.galaxy', 'a')
357 infof.write('\nOM: CLI options DEBUG START:\n') 365 infof.write('\nOM: CLI options DEBUG START:\n')
358 infof.write(options.__repr__()) 366 infof.write(options.__repr__())
359 infof.write('\nOM: CLI options DEBUG END\n') 367 infof.write('\nOM: CLI options DEBUG END\n')
360 368
361 if __name__=="__main__": __main__() 369 if __name__ == "__main__":
370 __main__()