def sate_main(argv=sys.argv): '''Returns (True, dir, temp_fs) on successful execution or raises an exception. Where `dir` is either None or the undeleted directory of temporary files. and `temp_fs` is is the TempFS object used to create `dir` (if `dir` is not None) Note that if `argv` is sys.argv then the first element will be skipped, but if it is not the sys.argv list then the first element will be interpretted as an argument (and will NOT be skipped). ''' _START_TIME = time.time() usage = """usage: %prog [options] <settings_file1> <settings_file2> ...""" parser = optparse.OptionParser(usage=usage, description=PROGRAM_LONG_DESCRIPTION, formatter=IndentedHelpFormatterWithNL(), version="%s v%s" % (PROGRAM_NAME, PROGRAM_VERSION)) user_config = get_configuration() command_line_group = user_config.get('commandline') command_line_group.add_to_optparser(parser) sate_group = user_config.get('sate') sate_group.add_to_optparser(parser) group = optparse.OptionGroup(parser, "SATe tools extra options") group.add_option('--tree-estimator-model', type='string', dest='tree_estimator_model', help='Do not use this option.') parser.add_option_group(group) if argv == sys.argv: (options, args) = parser.parse_args(argv[1:]) else: (options, args) = parser.parse_args(argv) #if options.multilocus: # sys.exit("SATe: Multilocus mode is disabled in this release.") if options.tree_estimator_model and options.tree_estimator and len( args) == 0: if options.tree_estimator.lower() == 'raxml': user_config.raxml.model = options.tree_estimator_model elif options.tree_estimator.lower() == 'fasttree': user_config.fasttree.model = options.tree_estimator_model config_filenames = list(args) for fn in config_filenames: if fn[0] == '"' and fn[-1] == '"': fn = fn[1:-1] if not os.path.exists(fn): raise Exception( 'The configuration (settings) file "%s" does not exist' % fn) try: user_config.read_config_filepath(fn) except: raise Exception( 'The file "%s" does not appear to be a valid configuration file format. It lacks section headers.' % fn) user_config.set_values_from_dict(options.__dict__) command_line_group.job = coerce_string_to_nice_outfilename( command_line_group.job, 'Job', 'satejob') if user_config.commandline.auto or (user_config.commandline.untrusted): if user_config.commandline.input is None: sys.exit("ERROR: Input file(s) not specified.") from sate.usersettingclasses import get_list_of_seq_filepaths_from_dir from sate.alignment import summary_stats_from_parse try: if user_config.commandline.multilocus: fn_list = get_list_of_seq_filepaths_from_dir( user_config.commandline.input) else: fn_list = [user_config.commandline.input] datatype_list = [user_config.commandline.datatype.upper()] careful_parse = user_config.commandline.untrusted summary_stats = summary_stats_from_parse( fn_list, datatype_list, careful_parse=careful_parse) except: if user_config.commandline.auto: MESSENGER.send_error( "Error reading input while setting options for the --auto mode\n" ) else: MESSENGER.send_error("Error reading input\n") raise if user_config.commandline.auto: user_config.commandline.auto = False auto_opts = get_auto_defaults_from_summary_stats( summary_stats[0], summary_stats[1], summary_stats[2]) user_config.get('sate').set_values_from_dict(auto_opts['sate']) user_config.get('commandline').set_values_from_dict( auto_opts['commandline']) user_config.get('fasttree').set_values_from_dict( auto_opts['fasttree']) if user_config.commandline.raxml_search_after: if user_config.sate.tree_estimator.upper() != 'FASTTREE': sys.exit( "ERROR: the 'raxml_search_after' option is only supported when the tree_estimator is FastTree" ) exportconfig = command_line_group.exportconfig if exportconfig: command_line_group.exportconfig = None user_config.save_to_filepath(exportconfig) ### TODO: wrap up in messaging system sys.stdout.write( 'Configuration written to "%s". Exiting successfully.\n' % exportconfig) return True, None, None if user_config.commandline.input is None: sys.exit("ERROR: Input file(s) not specified.") # note: need to read sequence files first to allow SateProducts to # correctly self-configure user_config.read_seq_filepaths( src=user_config.commandline.input, multilocus=user_config.commandline.multilocus) sate_products = filemgr.SateProducts(user_config) export_config_as_temp = True if export_config_as_temp: name_cfg = sate_products.get_abs_path_for_tag('sate_config.txt') command_line_group.exportconfig = None user_config.save_to_filepath(name_cfg) MESSENGER.send_info('Configuration written to "%s".\n' % name_cfg) MESSENGER.run_log_streams.append(sate_products.run_log_stream) MESSENGER.err_log_streams.append(sate_products.err_log_stream) temp_dir, temp_fs = run_sate_from_config(user_config, sate_products) _TIME_SPENT = time.time() - _START_TIME MESSENGER.send_info("Total time spent: %ss" % _TIME_SPENT) return True, temp_dir, temp_fs
def finish_sate_execution(sate_team, user_config, temporaries_dir, multilocus_dataset, sate_products): global _RunningJobs # get the RAxML model #TODO: this should check for the tree_estimator. Currently we only support raxml, so this works... model = user_config.raxml.model options = user_config.commandline user_config.save_to_filepath(os.path.join(temporaries_dir, 'last_used.cfg')) if options.timesfile: f = open_with_intermediates(options.timesfile, 'a') f.close() set_timing_log_filepath(options.timesfile) ############################################################################ # We must read the incoming tree in before we call the get_sequences_for_sate # function that relabels that taxa in the dataset ###### alignment_as_tmp_filename_to_report = None tree_as_tmp_filename_to_report = None tree_file = options.treefile if tree_file: if not os.path.exists(tree_file): raise Exception('The tree file "%s" does not exist' % tree_file) tree_f = open(tree_file, 'rU') MESSENGER.send_info('Reading starting trees from "%s"...' % tree_file) try: tree_list = read_and_encode_splits(multilocus_dataset.dataset, tree_f, starting_tree=True) except KeyError: MESSENGER.send_error( "Error in reading the treefile, probably due to a name in the tree that does not match the names in the input sequence files.\n" ) raise except: MESSENGER.send_error("Error in reading the treefile.\n") raise tree_f.close() if len(tree_list) > 1: MESSENGER.send_warning( '%d starting trees found in "%s". The first tree will be used.' % (len(tree_list), tree_file)) starting_tree = tree_list[0] score = None tree_as_tmp_filename_to_report = tree_file ############################################################################ # This will relabel the taxa if they have problematic names ##### multilocus_dataset.relabel_for_sate() ############################################################################ # This ensures all nucleotide data is DNA internally ##### restore_to_rna = False if user_config.commandline.datatype.upper() == 'RNA': multilocus_dataset.convert_rna_to_dna() user_config.commandline.datatype = 'DNA' restore_to_rna = True export_names = True if export_names: try: name_filename = sate_products.get_abs_path_for_tag( 'name_translation.txt') name_output = open(name_filename, 'w') safe2real = multilocus_dataset.safe_to_real_names safe_list = safe2real.keys() safe_list.sort() for safe in safe_list: orig = safe2real[safe][0] name_output.write("%s\n%s\n\n" % (safe, orig)) name_output.close() MESSENGER.send_info( "Name translation information saved to %s as safe name, original name, blank line format." % name_filename) except: MESSENGER.send_info( "Error exporting saving name translation to %s" % name_filename) if options.aligned: options.aligned = all([i.is_aligned() for i in multilocus_dataset]) ############################################################################ # Launch threads to do work ##### sate_config = user_config.get("sate") start_worker(sate_config.num_cpus) ############################################################################ # Be prepared to kill any long running jobs ##### prev_signals = [] for sig in [ signal.SIGTERM, signal.SIGABRT, signal.SIGINT ]: # signal.SIGABRT, signal.SIGBUS, signal.SIGINT, signal.SIGKILL, signal.SIGSTOP]: prev_handler = signal.signal(sig, killed_handler) prev_signals.append((sig, prev_handler)) try: if (not options.two_phase) and tree_file: # getting the newick string here will allow us to get a string that is in terms of the correct taxon labels starting_tree_str = starting_tree.compose_newick() else: if not options.two_phase: MESSENGER.send_info( "Creating a starting tree for the SATe algorithm...") if (options.two_phase) or (not options.aligned): MESSENGER.send_info( "Performing initial alignment of the entire data matrix..." ) init_aln_dir = os.path.join(temporaries_dir, 'init_aln') init_aln_dir = sate_team.temp_fs.create_subdir(init_aln_dir) delete_aln_temps = not (options.keeptemp and options.keepalignmenttemps) new_alignment_list = [] aln_job_list = [] for unaligned_seqs in multilocus_dataset: job = sate_team.aligner.create_job( unaligned_seqs, tmp_dir_par=init_aln_dir, context_str="initalign", delete_temps=delete_aln_temps) aln_job_list.append(job) _RunningJobs = aln_job_list for job in aln_job_list: jobq.put(job) for job in aln_job_list: new_alignment = job.get_results() new_alignment_list.append(new_alignment) _RunningJobs = None for locus_index, new_alignment in enumerate( new_alignment_list): multilocus_dataset[locus_index] = new_alignment if delete_aln_temps: sate_team.temp_fs.remove_dir(init_aln_dir) else: MESSENGER.send_info( "Input sequences assumed to be aligned (based on sequence lengths)." ) MESSENGER.send_info( "Performing initial tree search to get starting tree...") init_tree_dir = os.path.join(temporaries_dir, 'init_tree') init_tree_dir = sate_team.temp_fs.create_subdir(init_tree_dir) delete_tree_temps = not options.keeptemp job = sate_team.tree_estimator.create_job( multilocus_dataset, tmp_dir_par=init_tree_dir, num_cpus=sate_config.num_cpus, context_str="inittree", delete_temps=delete_tree_temps, sate_products=sate_products, step_num='initialsearch') _RunningJobs = job jobq.put(job) score, starting_tree_str = job.get_results() score = TransformScore(multilocus_dataset, score).execute( ) # MAN: need to transform score (ml) to our composite 5 objective score: simg, simng, sp, gap, ml _RunningJobs = None alignment_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output( "initialsearch", TEMP_SEQ_ALIGNMENT_TAG, allow_existing=True) tree_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output( "initialsearch", TEMP_TREE_TAG, allow_existing=True) if delete_tree_temps: sate_team.temp_fs.remove_dir(init_tree_dir) _LOG.debug('We have the tree and whole_alignment, partitions...') sate_config_dict = sate_config.dict() if options.keeptemp: sate_config_dict['keep_iteration_temporaries'] = True if options.keepalignmenttemps: sate_config_dict['keep_realignment_temporaries'] = True job = SateJob( multilocus_dataset=multilocus_dataset, sate_team=sate_team, name=options.job, status_messages=MESSENGER.send_info, score=score, # MAN: to init best_score **sate_config_dict) job.tree_str = starting_tree_str job.curr_iter_align_tmp_filename = alignment_as_tmp_filename_to_report job.curr_iter_tree_tmp_filename = tree_as_tmp_filename_to_report if score is not None: job.store_optimum_results( new_multilocus_dataset=multilocus_dataset, new_tree_str=starting_tree_str, new_score=score, curr_timestamp=time.time()) if options.two_phase: MESSENGER.send_info( "Exiting with the initial tree because the SATe algorithm is avoided when the --two-phase option is used." ) else: _RunningJobs = job MESSENGER.send_info("Starting SATe algorithm on initial tree...") job.run(tmp_dir_par=temporaries_dir, sate_products=sate_products) _RunningJobs = None if job.return_final_tree_and_alignment: alignment_as_tmp_filename_to_report = job.curr_iter_align_tmp_filename else: alignment_as_tmp_filename_to_report = job.best_alignment_tmp_filename if user_config.commandline.raxml_search_after: raxml_model = user_config.raxml.model.strip() if not raxml_model: dt = user_config.commandline.datatype mf = sate_team.tree_estimator.model ms = fasttree_to_raxml_model_str(dt, mf) sate_team.raxml_tree_estimator.model = ms rte = sate_team.raxml_tree_estimator MESSENGER.send_info( "Performing post-processing tree search in RAxML...") post_tree_dir = os.path.join(temporaries_dir, 'post_tree') post_tree_dir = sate_team.temp_fs.create_subdir(post_tree_dir) delete_tree_temps = not options.keeptemp starting_tree = None if user_config.sate.start_tree_search_from_current: starting_tree = job.tree post_job = rte.create_job(job.multilocus_dataset, starting_tree=starting_tree, num_cpus=sate_config.num_cpus, context_str="postraxtree", tmp_dir_par=post_tree_dir, delete_temps=delete_tree_temps, sate_products=sate_products, step_num="postraxtree") _RunningJobs = post_job jobq.put(post_job) post_score, post_tree = post_job.get_results() _RunningJobs = None tree_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output( "postraxtree", TEMP_TREE_TAG, allow_existing=True) if delete_tree_temps: sate_team.temp_fs.remove_dir(post_tree_dir) job.tree_str = post_tree job.score = post_score if post_score > job.best_score: job.best_tree_str = post_tree job.best_score = post_score else: if job.return_final_tree_and_alignment: tree_as_tmp_filename_to_report = job.curr_iter_tree_tmp_filename else: tree_as_tmp_filename_to_report = job.best_tree_tmp_filename ####################################################################### # Restore original taxon names and RNA characters ##### job.multilocus_dataset.restore_taxon_names() if restore_to_rna: job.multilocus_dataset.convert_dna_to_rna() user_config.commandline.datatype = 'RNA' assert len(sate_products.alignment_streams) == len( job.multilocus_dataset) for i, alignment in enumerate(job.multilocus_dataset): alignment_stream = sate_products.alignment_streams[i] MESSENGER.send_info("Writing resulting alignment to %s" % alignment_stream.name) alignment.write(alignment_stream, file_format="FASTA") alignment_stream.close() MESSENGER.send_info("Writing resulting tree to %s" % sate_products.tree_stream.name) tree_str = job.tree.compose_newick() sate_products.tree_stream.write("%s;\n" % tree_str) #outtree_fn = options.result #if outtree_fn is None: # if options.multilocus: # outtree_fn = os.path.join(seqdir, "combined_%s.tre" % options.job) # else: # outtree_fn = aln_filename + ".tre" #MESSENGER.send_info("Writing resulting tree to %s" % outtree_fn) #tree_str = job.tree.compose_newick() #sate_products.tree_stream.write("%s;\n" % tree_str) MESSENGER.send_info("Writing resulting likelihood score to %s" % sate_products.score_stream.name) sate_products.score_stream.write("%s\n" % job.score) if alignment_as_tmp_filename_to_report is not None: MESSENGER.send_info( 'The resulting alignment (with the names in a "safe" form) was first written as the file "%s"' % alignment_as_tmp_filename_to_report) if tree_as_tmp_filename_to_report is not None: MESSENGER.send_info( 'The resulting tree (with the names in a "safe" form) was first written as the file "%s"' % tree_as_tmp_filename_to_report) finally: for el in prev_signals: sig, prev_handler = el if prev_handler is None: signal.signal(sig, signal.SIG_DFL) else: signal.signal(sig, prev_handler)
rc, temp_dir, temp_fs = sate_main() if not rc: raise ValueError("Unknown SATe execution error") if (temp_dir is not None) and (os.path.exists(temp_dir)): MESSENGER.send_info( "Note that temporary files from the run have not been deleted, they can be found in:\n '%s'\n" % temp_dir) if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir): MESSENGER.send_info(''' If you cannot see this directory in the Finder application, you may want to use the 'open' command executed from a Terminal. You can do this by launching the /Applications/Utilities/Terminal program and then typing open '%s' followed by a return at the prompt. If the argument to the open command is a directory, then it should open a Finder window in the directory (even if that directory is hidden by default). ''' % temp_dir) except Exception, x: if _DEVELOPER: raise message = "SATe is exiting because of an error:\n%s " % str(x) try: from sate import MESSENGER MESSENGER.send_error(message) except: sys.stderr.write(message) sys.exit(1)
_SATE_DEVELOPER = os.environ.get('SATE_DEVELOPER') _DEVELOPER = _SATE_DEVELOPER and _SATE_DEVELOPER != '0' try: rc, temp_dir, temp_fs = sate_main() if not rc: raise ValueError("Unknown SATe execution error") if (temp_dir is not None) and (os.path.exists(temp_dir)): MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n '%s'\n" % temp_dir) if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir): MESSENGER.send_info(''' If you cannot see this directory in the Finder application, you may want to use the 'open' command executed from a Terminal. You can do this by launching the /Applications/Utilities/Terminal program and then typing open '%s' followed by a return at the prompt. If the argument to the open command is a directory, then it should open a Finder window in the directory (even if that directory is hidden by default). ''' % temp_dir) except Exception, x: if _DEVELOPER: raise message = "SATe is exiting because of an error:\n%s " % str(x) try: from sate import MESSENGER MESSENGER.send_error(message) except: sys.stderr.write(message) sys.exit(1)
def sate_main(argv=sys.argv): '''Returns (True, dir, temp_fs) on successful execution or raises an exception. Where `dir` is either None or the undeleted directory of temporary files. and `temp_fs` is is the TempFS object used to create `dir` (if `dir` is not None) Note that if `argv` is sys.argv then the first element will be skipped, but if it is not the sys.argv list then the first element will be interpretted as an argument (and will NOT be skipped). ''' _START_TIME = time.time() usage = """usage: %prog [options] <settings_file1> <settings_file2> ...""" parser = optparse.OptionParser(usage=usage, description=PROGRAM_LONG_DESCRIPTION, formatter=IndentedHelpFormatterWithNL(), version="%s v%s" % (PROGRAM_NAME, PROGRAM_VERSION)) user_config = get_configuration() command_line_group = user_config.get('commandline') command_line_group.add_to_optparser(parser) sate_group = user_config.get('sate') sate_group.add_to_optparser(parser) group = optparse.OptionGroup(parser, "SATe tools extra options") group.add_option('--tree-estimator-model', type='string', dest='tree_estimator_model', help='Do not use this option.') parser.add_option_group(group) if argv == sys.argv: (options, args) = parser.parse_args(argv[1:]) else: (options, args) = parser.parse_args(argv) #if options.multilocus: # sys.exit("SATe: Multilocus mode is disabled in this release.") if options.tree_estimator_model and options.tree_estimator and len(args) == 0: if options.tree_estimator.lower() == 'raxml': user_config.raxml.model = options.tree_estimator_model elif options.tree_estimator.lower() == 'fasttree': user_config.fasttree.model = options.tree_estimator_model config_filenames = list(args) for fn in config_filenames: if fn[0] == '"' and fn[-1] == '"': fn = fn[1:-1] if not os.path.exists(fn): raise Exception('The configuration (settings) file "%s" does not exist' % fn) try: user_config.read_config_filepath(fn) except: raise Exception('The file "%s" does not appear to be a valid configuration file format. It lacks section headers.' % fn) user_config.set_values_from_dict(options.__dict__) command_line_group.job = coerce_string_to_nice_outfilename(command_line_group.job, 'Job', 'satejob') if user_config.commandline.auto or (user_config.commandline.untrusted): if user_config.commandline.input is None: sys.exit("ERROR: Input file(s) not specified.") from sate.usersettingclasses import get_list_of_seq_filepaths_from_dir from sate.alignment import summary_stats_from_parse try: if user_config.commandline.multilocus: fn_list = get_list_of_seq_filepaths_from_dir(user_config.commandline.input) else: fn_list = [user_config.commandline.input] datatype_list = [user_config.commandline.datatype.upper()] careful_parse = user_config.commandline.untrusted summary_stats = summary_stats_from_parse(fn_list, datatype_list, careful_parse=careful_parse) except: if user_config.commandline.auto: MESSENGER.send_error("Error reading input while setting options for the --auto mode\n") else: MESSENGER.send_error("Error reading input\n") raise if user_config.commandline.auto: user_config.commandline.auto = False auto_opts = get_auto_defaults_from_summary_stats(summary_stats[0], summary_stats[1], summary_stats[2]) user_config.get('sate').set_values_from_dict(auto_opts['sate']) user_config.get('commandline').set_values_from_dict(auto_opts['commandline']) user_config.get('fasttree').set_values_from_dict(auto_opts['fasttree']) if user_config.commandline.raxml_search_after: if user_config.sate.tree_estimator.upper() != 'FASTTREE': sys.exit("ERROR: the 'raxml_search_after' option is only supported when the tree_estimator is FastTree") exportconfig = command_line_group.exportconfig if exportconfig: command_line_group.exportconfig = None user_config.save_to_filepath(exportconfig) ### TODO: wrap up in messaging system sys.stdout.write('Configuration written to "%s". Exiting successfully.\n' % exportconfig ) return True, None, None if user_config.commandline.input is None: sys.exit("ERROR: Input file(s) not specified.") # note: need to read sequence files first to allow SateProducts to # correctly self-configure user_config.read_seq_filepaths(src=user_config.commandline.input, multilocus=user_config.commandline.multilocus) sate_products = filemgr.SateProducts(user_config) export_config_as_temp = True if export_config_as_temp: name_cfg = sate_products.get_abs_path_for_tag('sate_config.txt') command_line_group.exportconfig = None user_config.save_to_filepath(name_cfg) MESSENGER.send_info('Configuration written to "%s".\n' % name_cfg ) MESSENGER.run_log_streams.append(sate_products.run_log_stream) MESSENGER.err_log_streams.append(sate_products.err_log_stream) temp_dir, temp_fs = run_sate_from_config(user_config, sate_products) _TIME_SPENT = time.time() - _START_TIME MESSENGER.send_info("Total time spent: %ss" % _TIME_SPENT) return True, temp_dir, temp_fs
def finish_sate_execution(sate_team, user_config, temporaries_dir, multilocus_dataset, sate_products): global _RunningJobs # get the RAxML model #TODO: this should check for the tree_estimator. Currently we only support raxml, so this works... model = user_config.raxml.model options = user_config.commandline user_config.save_to_filepath(os.path.join(temporaries_dir, 'last_used.cfg')) if options.timesfile: f = open_with_intermediates(options.timesfile, 'a') f.close() set_timing_log_filepath(options.timesfile) ############################################################################ # We must read the incoming tree in before we call the get_sequences_for_sate # function that relabels that taxa in the dataset ###### alignment_as_tmp_filename_to_report = None tree_as_tmp_filename_to_report = None tree_file = options.treefile if tree_file: if not os.path.exists(tree_file): raise Exception('The tree file "%s" does not exist' % tree_file) tree_f = open(tree_file, 'rU') MESSENGER.send_info('Reading starting trees from "%s"...' % tree_file) try: tree_list = read_and_encode_splits(multilocus_dataset.dataset, tree_f, starting_tree=True) except KeyError: MESSENGER.send_error("Error in reading the treefile, probably due to a name in the tree that does not match the names in the input sequence files.\n") raise except: MESSENGER.send_error("Error in reading the treefile.\n") raise tree_f.close() if len(tree_list) > 1: MESSENGER.send_warning('%d starting trees found in "%s". The first tree will be used.' % (len(tree_list), tree_file)) starting_tree = tree_list[0] score = None tree_as_tmp_filename_to_report = tree_file ############################################################################ # This will relabel the taxa if they have problematic names ##### multilocus_dataset.relabel_for_sate() ############################################################################ # This ensures all nucleotide data is DNA internally ##### restore_to_rna = False if user_config.commandline.datatype.upper() == 'RNA': multilocus_dataset.convert_rna_to_dna() user_config.commandline.datatype = 'DNA' restore_to_rna = True export_names = True if export_names: try: name_filename = sate_products.get_abs_path_for_tag('name_translation.txt') name_output = open(name_filename, 'w') safe2real = multilocus_dataset.safe_to_real_names safe_list = safe2real.keys() safe_list.sort() for safe in safe_list: orig = safe2real[safe][0] name_output.write("%s\n%s\n\n" % (safe, orig)) name_output.close() MESSENGER.send_info("Name translation information saved to %s as safe name, original name, blank line format." % name_filename) except: MESSENGER.send_info("Error exporting saving name translation to %s" % name_filename) if options.aligned: options.aligned = all( [i.is_aligned() for i in multilocus_dataset] ) ############################################################################ # Launch threads to do work ##### sate_config = user_config.get("sate") start_worker(sate_config.num_cpus) ############################################################################ # Be prepared to kill any long running jobs ##### prev_signals = [] for sig in [signal.SIGTERM, signal.SIGABRT, signal.SIGINT]: # signal.SIGABRT, signal.SIGBUS, signal.SIGINT, signal.SIGKILL, signal.SIGSTOP]: prev_handler = signal.signal(sig, killed_handler) prev_signals.append((sig, prev_handler)) try: if (not options.two_phase) and tree_file: # getting the newick string here will allow us to get a string that is in terms of the correct taxon labels starting_tree_str = starting_tree.compose_newick() else: if not options.two_phase: MESSENGER.send_info("Creating a starting tree for the SATe algorithm...") if (options.two_phase) or (not options.aligned): MESSENGER.send_info("Performing initial alignment of the entire data matrix...") init_aln_dir = os.path.join(temporaries_dir, 'init_aln') init_aln_dir = sate_team.temp_fs.create_subdir(init_aln_dir) delete_aln_temps = not (options.keeptemp and options.keepalignmenttemps) new_alignment_list= [] aln_job_list = [] for unaligned_seqs in multilocus_dataset: job = sate_team.aligner.create_job(unaligned_seqs, tmp_dir_par=init_aln_dir, context_str="initalign", delete_temps=delete_aln_temps) aln_job_list.append(job) _RunningJobs = aln_job_list for job in aln_job_list: jobq.put(job) for job in aln_job_list: new_alignment = job.get_results() new_alignment_list.append(new_alignment) _RunningJobs = None for locus_index, new_alignment in enumerate(new_alignment_list): multilocus_dataset[locus_index] = new_alignment if delete_aln_temps: sate_team.temp_fs.remove_dir(init_aln_dir) else: MESSENGER.send_info("Input sequences assumed to be aligned (based on sequence lengths).") MESSENGER.send_info("Performing initial tree search to get starting tree...") init_tree_dir = os.path.join(temporaries_dir, 'init_tree') init_tree_dir = sate_team.temp_fs.create_subdir(init_tree_dir) delete_tree_temps = not options.keeptemp job = sate_team.tree_estimator.create_job(multilocus_dataset, tmp_dir_par=init_tree_dir, num_cpus=sate_config.num_cpus, context_str="inittree", delete_temps=delete_tree_temps, sate_products=sate_products, step_num='initialsearch') _RunningJobs = job jobq.put(job) score, starting_tree_str = job.get_results() _RunningJobs = None alignment_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output("initialsearch", TEMP_SEQ_ALIGNMENT_TAG, allow_existing=True) tree_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output("initialsearch", TEMP_TREE_TAG, allow_existing=True) if delete_tree_temps: sate_team.temp_fs.remove_dir(init_tree_dir) _LOG.debug('We have the tree and whole_alignment, partitions...') sate_config_dict = sate_config.dict() if options.keeptemp: sate_config_dict['keep_iteration_temporaries'] = True if options.keepalignmenttemps: sate_config_dict['keep_realignment_temporaries'] = True job = SateJob(multilocus_dataset=multilocus_dataset, sate_team=sate_team, name=options.job, status_messages=MESSENGER.send_info, score=score, **sate_config_dict) job.tree_str = starting_tree_str job.curr_iter_align_tmp_filename = alignment_as_tmp_filename_to_report job.curr_iter_tree_tmp_filename = tree_as_tmp_filename_to_report if score is not None: job.store_optimum_results(new_multilocus_dataset=multilocus_dataset, new_tree_str=starting_tree_str, new_score=score, curr_timestamp=time.time()) if options.two_phase: MESSENGER.send_info("Exiting with the initial tree because the SATe algorithm is avoided when the --two-phase option is used.") else: _RunningJobs = job MESSENGER.send_info("Starting SATe algorithm on initial tree...") job.run(tmp_dir_par=temporaries_dir, sate_products=sate_products) _RunningJobs = None if job.return_final_tree_and_alignment: alignment_as_tmp_filename_to_report = job.curr_iter_align_tmp_filename else: alignment_as_tmp_filename_to_report = job.best_alignment_tmp_filename if user_config.commandline.raxml_search_after: raxml_model = user_config.raxml.model.strip() if not raxml_model: dt = user_config.commandline.datatype mf = sate_team.tree_estimator.model ms = fasttree_to_raxml_model_str(dt, mf) sate_team.raxml_tree_estimator.model = ms rte = sate_team.raxml_tree_estimator MESSENGER.send_info("Performing post-processing tree search in RAxML...") post_tree_dir = os.path.join(temporaries_dir, 'post_tree') post_tree_dir = sate_team.temp_fs.create_subdir(post_tree_dir) delete_tree_temps = not options.keeptemp starting_tree = None if user_config.sate.start_tree_search_from_current: starting_tree = job.tree post_job = rte.create_job(job.multilocus_dataset, starting_tree=starting_tree, num_cpus=sate_config.num_cpus, context_str="postraxtree", tmp_dir_par=post_tree_dir, delete_temps=delete_tree_temps, sate_products=sate_products, step_num="postraxtree") _RunningJobs = post_job jobq.put(post_job) post_score, post_tree = post_job.get_results() _RunningJobs = None tree_as_tmp_filename_to_report = sate_products.get_abs_path_for_iter_output("postraxtree", TEMP_TREE_TAG, allow_existing=True) if delete_tree_temps: sate_team.temp_fs.remove_dir(post_tree_dir) job.tree_str = post_tree job.score = post_score if post_score > job.best_score: job.best_tree_str = post_tree job.best_score = post_score else: if job.return_final_tree_and_alignment: tree_as_tmp_filename_to_report = job.curr_iter_tree_tmp_filename else: tree_as_tmp_filename_to_report = job.best_tree_tmp_filename ####################################################################### # Restore original taxon names and RNA characters ##### job.multilocus_dataset.restore_taxon_names() if restore_to_rna: job.multilocus_dataset.convert_dna_to_rna() user_config.commandline.datatype = 'RNA' assert len(sate_products.alignment_streams) == len(job.multilocus_dataset) for i, alignment in enumerate(job.multilocus_dataset): alignment_stream = sate_products.alignment_streams[i] MESSENGER.send_info("Writing resulting alignment to %s" % alignment_stream.name) alignment.write(alignment_stream, file_format="FASTA") alignment_stream.close() MESSENGER.send_info("Writing resulting tree to %s" % sate_products.tree_stream.name) tree_str = job.tree.compose_newick() sate_products.tree_stream.write("%s;\n" % tree_str) #outtree_fn = options.result #if outtree_fn is None: # if options.multilocus: # outtree_fn = os.path.join(seqdir, "combined_%s.tre" % options.job) # else: # outtree_fn = aln_filename + ".tre" #MESSENGER.send_info("Writing resulting tree to %s" % outtree_fn) #tree_str = job.tree.compose_newick() #sate_products.tree_stream.write("%s;\n" % tree_str) MESSENGER.send_info("Writing resulting likelihood score to %s" % sate_products.score_stream.name) sate_products.score_stream.write("%s\n" % job.score) if alignment_as_tmp_filename_to_report is not None: MESSENGER.send_info('The resulting alignment (with the names in a "safe" form) was first written as the file "%s"' % alignment_as_tmp_filename_to_report) if tree_as_tmp_filename_to_report is not None: MESSENGER.send_info('The resulting tree (with the names in a "safe" form) was first written as the file "%s"' % tree_as_tmp_filename_to_report) finally: for el in prev_signals: sig, prev_handler = el if prev_handler is None: signal.signal(sig, signal.SIG_DFL) else: signal.signal(sig, prev_handler)