Mercurial > repos > malex > raxml
diff raxml.py @ 0:d95d87f40f47 draft default tip
Uploaded the first beta.
| author | malex |
|---|---|
| date | Tue, 02 Oct 2012 17:35:46 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raxml.py Tue Oct 02 17:35:46 2012 -0400 @@ -0,0 +1,365 @@ +#!/usr/bin/env python +""" +Runs RAxML on a sequence file. +For use with RAxML version 7.3.0 + +usage: + <!-- raxmlHPC-PTHREADS-SSE3 -T 2 -f c -m GTRGAMMA -F -s "/Users/om/Downloads/rana.phy" -n rana_red -w "/Users/om/Downloads/" 0 + ## raxmlHPC-PTHREADS-SSE3 -T 2 -m GTRGAMMA -n test -p 323483 -s reduced.phy + command>raxmlHPC-HYBRID-SSE3 -T 4 -f ${search_algorithm} -m ${smodel} -N ${repeats} -o "${html_outfile.files_path}" -s "$input1" +""" +import os, shutil, subprocess, sys, optparse, fnmatch, glob + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit() + +def getint(name): + basename = name.partition('RUN.') + if basename[2] != '': + num = basename[2] + return int(num) + +def __main__(): + usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]" + + # Parse the primary wrapper's command line options + parser = optparse.OptionParser(usage = usage) + # raxml binary name, hardcoded in the xml file + parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run") + # (-a) + parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file") + # (-A) + parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model") + # (-b) + parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed") + # (-c) + parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories") + # (-d) + parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree") + # (-D) + parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion") + # (-e) + parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)") + # (-E) + parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name") + # (-f) + parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm") + # (-F) + parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models") + # (-g) + parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name") + # (-G) + parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics") + # (-i) + parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting") + # (-I) + parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis") + # (-J) + parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus") + # (-k) + parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths") + # (-K) + parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model") + # (-m) + parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type") + parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model") + parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences") + parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix") + # (-n) + parser.add_option("--name", action="store", type="string", dest="name", help="Run Name") + # (-N/#) + parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", help="Number of alternative runs") + 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") + # (-M) + parser.add_option("--estimate_individual_branch_lengths", action="store_true", dest="estimate_individual_branch_lengths", help="Estimate individual branch lengths") + # (-o) + parser.add_option("--outgroup_name", action="store", type="string", dest="outgroup_name", help="Outgroup Name") + # (-O) + parser.add_option("--disable_undetermined_seq_check", action="store_true", dest="disable_undetermined_seq_check", help="Disable undetermined sequence check") + # (-p) + parser.add_option("--random_seed", action="store", type="int", dest="random_seed", help="Random Number Seed") + # (-P) + parser.add_option("--external_protein_model", action="store", type="string", dest="external_protein_model", help="External Protein Model") + # (-q) + parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File") + # (-r) + parser.add_option("--constraint_file", action="store", type="string", dest="constraint_file", help="Constraint File") + # (-R) + parser.add_option("--bin_model_parameter_file", action="store", type="string", dest="bin_model_parameter_file", help="Constraint File") + # (-s) + parser.add_option("--source", action="store", type="string", dest="source", help="Input file") + # (-S) + parser.add_option("--secondary_structure_file", action="store", type="string", dest="secondary_structure_file", help="Secondary structure file") + # (-t) + parser.add_option("--starting_tree", action="store", type="string", dest="starting_tree", help="Starting Tree") + # (-T) + parser.add_option("--threads", action="store", type="int", dest="threads", help="Number of threads to use") + # (-u) + parser.add_option("--use_median_approximation", action="store_true", dest="use_median_approximation", help="Use median approximation") + # (-U) + parser.add_option("--save_memory_gappy_alignments", action="store_true", dest="save_memory_gappy_alignments", help="Save memory in large gapped alignments") + # (-V) + parser.add_option("--disable_rate_heterogeneity", action="store_true", dest="disable_rate_heterogeneity", help="Disable rate heterogeneity") + # (-W) + parser.add_option("--sliding_window_size", action="store", type="string", dest="sliding_window_size", help="Sliding window size") + # (-x) + parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed") + # (-y) + parser.add_option("--parsimony_starting_tree_only", action="store_true", dest="parsimony_starting_tree_only", help="Generate a parsimony starting tree only") + # (-z) + parser.add_option("--file_multiple_trees", action="store", type="string", dest="file_multiple_trees", help="Multiple Trees File") + + (options, args) = parser.parse_args() + cmd = [] + + # Required parameters + binary = options.binary + cmd.append(binary) + # Threads + threads = "-T %d" % options.threads + cmd.append(threads) + # Source + source = "-s %s" % options.source + cmd.append(source) + #Hardcode to "galaxy" first to simplify the output part of the wrapper + #name = "-n %s" % options.name + name = "-n galaxy" + cmd.append(name) + ## Model + model_type = options.model_type + base_model = options.base_model + aa_search_matrix = options.aa_search_matrix + aa_empirical_freq = options.aa_empirical_freq + if model_type == 'aminoacid': + model = "-m %s%s" % (base_model, aa_search_matrix) + if aa_empirical_freq: + model = "-m %s%s%s" % (base_model, aa_search_matrix, 'F') + # (-P) + if options.external_protein_model: + external_protein_model = "-P %s" % options.external_protein_model + cmd.append(external_protein_model) + else: + model = "-m %s" % base_model + cmd.append(model) + if model == "GTRCAT": + # (-c) + if options.numofcats: + numofcats = "-c %d" % options.numofcats + cmd.append(numofcats) + # Optional parameters + if options.number_of_runs_bootstop: + number_of_runs_bootstop = "-N %s" % options.number_of_runs_bootstop + cmd.append(number_of_runs_bootstop) + else: + number_of_runs_bootstop = '' + if options.number_of_runs: + number_of_runs_opt = "-N %d" % options.number_of_runs + cmd.append(number_of_runs_opt) + else: + number_of_runs_opt = 0 + # (-a) + if options.weightfile: + weightfile = "-a %s" % options.weightfile + cmd.append(weightfile) + # (-A) + if options.secondary_structure_model: + secondary_structure_model = "-A %s" % options.secondary_structure_model + cmd.append(secondary_structure_model ) + # (-b) + if options.bootseed: + bootseed = "-b %d" % options.bootseed + cmd.append(bootseed) + else: + bootseed = 0 + # -C - doesn't work in pthreads version, skipped + if options.search_complete_random_tree: + cmd.append("-d") + if options.ml_search_convergence: + cmd.append("-D" ) + if options.model_opt_precision: + model_opt_precision = "-e %f" % options.model_opt_precision + cmd.append(model_opt_precision) + if options.excludefile: + excludefile = "-E %s" % options.excludefile + cmd.append(excludefile) + if options.search_algorithm: + search_algorithm = "-f %s" % options.search_algorithm + cmd.append(search_algorithm) + if options.save_memory_cat_model: + cmd.append("-F") + if options.groupingfile: + groupingfile = "-g %s" % options.groupingfile + cmd.append(groupingfile) + if options.enable_evol_heuristics: + enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics + cmd.append(enable_evol_heuristics ) + if options.initial_rearrangement_setting: + initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting + cmd.append(initial_rearrangement_setting) + if options.posterior_bootstopping_analysis: + posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis + cmd.append(posterior_bootstopping_analysis) + if options.majority_rule_consensus: + majority_rule_consensus = "-J %s" % options.majority_rule_consensus + cmd.append(majority_rule_consensus) + if options.print_branch_lengths: + cmd.append("-k") + if options.multistate_sub_model: + multistate_sub_model = "-K %s" % options.multistate_sub_model + cmd.append(multistate_sub_model) + if options.estimate_individual_branch_lengths: + cmd.append("-M") + if options.outgroup_name: + outgroup_name = "-o %s" % options.outgroup_name + cmd.append(outgroup_name) + if options.disable_undetermined_seq_check: + cmd.append("-O") + if options.random_seed: + random_seed = "-p %d" % options.random_seed + cmd.append(random_seed) + multiple_model = None + if options.multiple_model: + multiple_model = "-q %s" % options.multiple_model + cmd.append(multiple_model) + if options.constraint_file: + constraint_file = "-r %s" % options.constraint_file + cmd.append(constraint_file) + if options.bin_model_parameter_file: + bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy" + os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name ) + bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file + #Needs testing. Is the hardcoded name or the real path needed? + cmd.append(bin_model_parameter_file) + if options.secondary_structure_file: + secondary_structure_file = "-S %s" % options.secondary_structure_file + cmd.append(secondary_structure_file) + if options.starting_tree: + starting_tree = "-t %s" % options.starting_tree + cmd.append(starting_tree) + if options.use_median_approximation: + cmd.append("-u") + if options.save_memory_gappy_alignments: + cmd.append("-U") + if options.disable_rate_heterogeneity: + cmd.append("-V") + if options.sliding_window_size: + sliding_window_size = "-W %d" % options.sliding_window_size + cmd.append(sliding_window_size) + if options.rapid_bootstrap_random_seed: + rapid_bootstrap_random_seed = "-x %d" % options.rapid_bootstrap_random_seed + cmd.append(rapid_bootstrap_random_seed) + else: + rapid_bootstrap_random_seed = 0 + if options.parsimony_starting_tree_only: + cmd.append("-y") + if options.file_multiple_trees: + file_multiple_trees = "-z %s" % options.file_multiple_trees + cmd.append(file_multiple_trees) + + print "cmd list: ", cmd, "\n" + + full_cmd = " ".join(cmd) + print "Command string: %s" % full_cmd + + try: + proc = subprocess.Popen(args=full_cmd, shell=True, 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) + else: + sys.stdout.write(stdout) + sys.stdout.write(stderr) + + #Multiple runs - concatenate + if number_of_runs_opt > 0: + if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ): + runfiles = glob.glob('RAxML*RUN*') + runfiles.sort(key=getint) + # Logs + outfile = open('RAxML_log.galaxy','w') + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): + infile = open(filename, 'r') + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + infile.close() + outfile.close() + # Parsimony Trees + outfile = open('RAxML_parsimonyTree.galaxy','w') + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): + infile = open(filename, 'r') + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + infile.close() + outfile.close() + # Results + outfile = open('RAxML_result.galaxy','w') + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): + infile = open(filename, 'r') + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + infile.close() + outfile.close() + # Multiple Model Partition Files + if multiple_model: + files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*') + if len(files) > 0: + files.sort(key=getint) + outfile = open('RAxML_bestTreePartitions.galaxy','w') + # Best Tree Partitions + for filename in files: + if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): + infile = open(filename, 'r') + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + infile.close() + outfile.close() + else: + outfile = open('RAxML_bestTreePartitions.galaxy','w') + outfile.write("No partition files were produced.\n") + outfile.close() + + # Result Partitions + files = glob.glob('RAxML_result.galaxy.PARTITION.*') + if len(files) > 0: + files.sort(key=getint) + outfile = open('RAxML_resultPartitions.galaxy','w') + for filename in files: + if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): + infile = open(filename, 'r') + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + infile.close() + outfile.close() + else: + outfile = open('RAxML_resultPartitions.galaxy','w') + outfile.write("No partition files were produced.\n") + outfile.close() + + # DEBUG options + infof = open('RAxML_info.galaxy','a') + infof.write('\nOM: CLI options DEBUG START:\n') + infof.write(options.__repr__()) + infof.write('\nOM: CLI options DEBUG END\n') + +if __name__=="__main__": __main__()