Example #1
0
def coerce_string_to_nice_outfilename(p, reason, default):
    illegal_filename_pattern = re.compile(r'[^-_a-zA-Z0-9.]')
    j = "".join(illegal_filename_pattern.split(p))
    if not j:
        j = default
    if j != p:
        MESSENGER.send_warning('%s name changed from "%s" to "%s" (a safer name for filepath)' % (reason, p, j))
    return j
Example #2
0
def killed_handler(n, frame):
    global _RunningJobs
    if _RunningJobs:
        MESSENGER.send_warning("signal killed_handler called. Killing running jobs...\n")
        j = _RunningJobs
        j.kill()
    else:
        MESSENGER.send_warning("signal killed_handler called with no jobs running. Exiting.\n")
    sys.exit()
Example #3
0
def run_sate_from_config(user_config, sate_products):
    """
    Returns (None, None) if no temporary directory is left over from the run
    or returns (dir, temp_fs) where `dir` is the path to the temporary
    directory created for the scratch files and `temp_fs` is the TempFS
    instance used to create `dir`
    """

    multilocus_dataset = read_input_sequences(user_config.input_seq_filepaths,
            datatype=user_config.commandline.datatype,
            missing=user_config.commandline.missing)
    cmdline_options = user_config.commandline

    ############################################################################
    # Create the safe directory for temporaries
    # The general form of the directory is
    #   ${options.temporaries}/${options.job}/temp${RANDOM}
    ######
    par_dir = cmdline_options.temporaries
    if par_dir is None:
        par_dir = os.path.join(os.path.expanduser('~'), '.sate')
    cmdline_options.job = coerce_string_to_nice_outfilename(cmdline_options.job, "Job", "satejob")
    subdir = cmdline_options.job
    par_dir = os.path.abspath(os.path.join(par_dir, subdir))
    if not os.path.exists(par_dir):
        os.makedirs(par_dir) # this parent directory will not be deleted, so we don't store it in the sate_team.temp_fs

    sate_team = SateTeam(config=user_config)

    delete_dir = not cmdline_options.keeptemp

    temporaries_dir = sate_team.temp_fs.create_top_level_temp(parent=par_dir, prefix='temp')
    assert(os.path.exists(temporaries_dir))
    try:
        MESSENGER.send_info("Directory for temporary files created at %s" % temporaries_dir)
        finish_sate_execution(sate_team=sate_team,
                              user_config=user_config,
                              temporaries_dir=temporaries_dir,
                              multilocus_dataset=multilocus_dataset,
                              sate_products=sate_products)
    finally:
        if delete_dir:
            sate_team.temp_fs.remove_dir(temporaries_dir)
    if delete_dir:
        return None, None
    else:
        return temporaries_dir, sate_team.temp_fs
Example #4
0
def killed_handler(n, frame):
    global _RunningJobs
    if _RunningJobs:
        MESSENGER.send_warning("signal killed_handler called. Killing running jobs...\n")
        if isinstance(_RunningJobs, list):
            for j in _RunningJobs:
                j.kill()
                MESSENGER.send_warning("kill called...\n")
        else:
            j = _RunningJobs
            j.kill()
            MESSENGER.send_warning("kill called...\n")
    else:
        MESSENGER.send_warning("signal killed_handler called with no jobs running. Exiting.\n")
    sys.exit()
Example #5
0
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
    ######
    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)
        tree_list = read_and_encode_splits(multilocus_dataset.dataset, tree_f)
        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

    ############################################################################
    # This will relabel the taxa if they have problematic names
    #####
    multilocus_dataset.relabel_for_sate()

    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 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:
            MESSENGER.send_info("Performing initial tree search to get starting tree...")
            if 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= []
                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)
                    _RunningJobs = job
                    jobq.put(job)
                    new_alignment = job.get_results()
                    _RunningJobs = None
                    new_alignment_list.append(new_alignment)
                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)
            _RunningJobs = job
            jobq.put(job)
            score, starting_tree_str = job.get_results()
            _RunningJobs = None
            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,
                        **sate_config_dict)
        job.tree_str = starting_tree_str
        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())

        _RunningJobs = job
        MESSENGER.send_info("Starting SATe algorithm on initial tree...")
        job.run(tmp_dir_par=temporaries_dir)
        _RunningJobs = None
        job.multilocus_dataset.restore_taxon_names()
        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 final alignment to %s" % alignment_stream.name)
            alignment.write(alignment_stream, file_format="FASTA")
            alignment_stream.close()


        MESSENGER.send_info("Writing final 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 final tree to %s" % outtree_fn)
        #tree_str = job.tree.compose_newick()
        #sate_products.tree_stream.write("%s;\n" % tree_str)


        MESSENGER.send_info("Writing final likelihood score to %s" % sate_products.score_stream.name)
        sate_products.score_stream.write("%s\n" % job.score)
    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)
Example #6
0
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)
    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.")
    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')

    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.' % 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)

    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
Example #7
0
    import os
    import sys
    from sate.mainsate import sate_main
    from sate import MESSENGER
    _SATE_DEBUG = os.environ.get('SATE_DEBUG')
    _DEVELOPER = _SATE_DEBUG and _SATE_DEBUG != '0'

    if not _DEVELOPER:
        _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
Example #8
0
    def run(self, tmp_dir_par, sate_products=None):
        assert(os.path.exists(tmp_dir_par))

        self._reset_current_run_settings()
        self._reset_jobs()

        self.start_time = time.time()
        self.last_improvement_time = self.start_time

        num_non_update_iter = 0

        configuration = self.configuration()
        # Here we check if the max_subproblem_frac is more stringent than max_subproblem_size
        frac_max = int(math.ceil(self.max_subproblem_frac*self.tree.n_leaves))
        if frac_max > self.max_subproblem_size:
            configuration['max_subproblem_size'] = frac_max
        MESSENGER.send_info('Max subproblem set to {0}'.format(
                configuration['max_subproblem_size']))
        if configuration['max_subproblem_size'] >= self.tree.n_leaves:
            MESSENGER.send_warning('''\n
WARNING: you have specified a max subproblem ({0}) that is equal to or greater
    than the number of taxa ({0}). Thus, the SATe algorithm will not be invoked
    under the current configuration (i.e., no tree decomposition will occur).
    If you did not intend for this behavior (which you probably did not since
    you are using SATe) please adjust your settings for the max subproblem and
    try running SATe again. If you intended to use SATe to align your data with
    the specified aligner tool *without* any decomposition, you can ignore this
    message.\n'''.format(configuration['max_subproblem_size'],
                       self.tree.n_leaves))
        delete_iteration_temps = not self.keep_iteration_temporaries
        delete_realignment_temps = delete_iteration_temps or (not self.keep_realignment_temporaries)
        configuration['delete_temps'] = delete_realignment_temps

        while self._keep_iterating():
            record_timestamp(os.path.join(tmp_dir_par, 'start_sateiter_timestamp.txt'))

            # create a subdirectory for this iteration
            curr_iter_tmp_dir_par = os.path.join(tmp_dir_par, 'step' + str(self.current_iteration))
            curr_iter_tmp_dir_par = self.sate_team.temp_fs.create_subdir(curr_iter_tmp_dir_par)
            _LOG.debug('directory %s created' % curr_iter_tmp_dir_par)
            break_strategy_index = 0
            this_iter_score_improved = False

            while True:
                break_strategy =  self._get_break_strategy(break_strategy_index)
                if not bool(break_strategy):
                    break
                context_str = "iter%d-%s" % (self.current_iteration, break_strategy)
                # create a subdirectory for this iteration/break_strategy
                curr_tmp_dir_par = os.path.join(curr_iter_tmp_dir_par, break_strategy)
                curr_tmp_dir_par = self.sate_team.temp_fs.create_subdir(curr_tmp_dir_par)
                record_timestamp(os.path.join(curr_tmp_dir_par, 'start_align_timestamp.txt'))
                # Align (with decomposition...)
                self.status('Step %d. Realigning with decomposition strategy set to %s' % (self.current_iteration, break_strategy))
                if self.killed:
                    raise RuntimeError("SATe Job killed")
                tree_for_aligner = self.get_tree_copy()
                tree_for_aligner = self.get_tree_copy()
                aligner = SateAlignerJob(multilocus_dataset=self.multilocus_dataset,
                                         sate_team=self.sate_team,
                                         tree=tree_for_aligner,
                                         tmp_base_dir=curr_tmp_dir_par,
                                         reset_recursion_index=True,
                                         **configuration)
                self.sate_aligner_job = aligner
                aligner.launch_alignment(break_strategy=break_strategy,
                                         context_str=context_str)

                new_multilocus_dataset = aligner.get_results()
                self.sate_aligner_job = None
                del aligner


                record_timestamp(os.path.join(curr_tmp_dir_par, 'start_treeinference_timestamp.txt'))
                # Tree inference
                if self.start_tree_search_from_current:
                    start_from = self.tree
                else:
                    start_from = None
                self.status('Step %d. Alignment obtained. Tree inference beginning...' % (self.current_iteration))
                if self.killed:
                    raise RuntimeError("SATe Job killed")
                tbj = self.sate_team.tree_estimator.create_job(new_multilocus_dataset,
                                                               starting_tree=start_from,
                                                               num_cpus=self.num_cpus,
                                                               context_str=context_str + " tree",
                                                               tmp_dir_par=curr_tmp_dir_par,
                                                               delete_temps=delete_iteration_temps,
                                                               sate_products=sate_products,
                                                               step_num=self.current_iteration)
                prev_curr_align = self.curr_iter_align_tmp_filename
                prev_curr_tree = self.curr_iter_tree_tmp_filename
                self.curr_iter_align_tmp_filename = sate_products.get_abs_path_for_iter_output(self.current_iteration, TEMP_SEQ_ALIGNMENT_TAG, allow_existing=True)
                self.curr_iter_tree_tmp_filename = sate_products.get_abs_path_for_iter_output(self.current_iteration, TEMP_TREE_TAG, allow_existing=True)

                self.tree_build_job = tbj
                jobq.put(tbj)
                new_score, new_tree_str = tbj.get_results()
                self.tree_build_job = None
                del tbj
                if self.killed:
                    raise RuntimeError("SATe Job killed")

                record_timestamp(os.path.join(curr_tmp_dir_par, 'end_treeinference_timestamp.txt'))
                curr_timestamp = time.time()
                accept_iteration = False

                if self.score is None:
                    self.score = new_score

                if self.best_score is None or new_score > self.best_score:
                    self.store_optimum_results(new_multilocus_dataset,
                            new_tree_str,
                            new_score,
                            curr_timestamp)
                    this_iter_score_improved = True
                    accept_iteration = True

                if self._get_accept_mode(new_score=new_score, break_strategy_index=break_strategy_index) == AcceptMode.BLIND_MODE:
                    if self.blind_mode_is_final:
                        self.is_stuck_in_blind = True
                        if self.switch_to_blind_timestamp is None:
                            if self._blindmode_trigger:
                                _LOG.debug("Blind runmode trigger = %s" % self._blindmode_trigger)
                            self.switch_to_blind_iter = self.current_iteration
                            self.switch_to_blind_timestamp = curr_timestamp
                    accept_iteration = True

                if accept_iteration:
                    self.score = new_score
                    self.multilocus_dataset = new_multilocus_dataset
                    self.tree_str = new_tree_str
                    if this_iter_score_improved:
                        self.status('realignment accepted and score improved.')
                    else:
                        self.status('realignment accepted and despite the score not improving.')
                    # we do not want to continue to try different breaking strategies for this iteration so we break
                    self.status('current score: %s, best score: %s' % (self.score, self.best_score) )
                    break
                else:
                    self.status('realignment NOT accepted.')
                    self.curr_iter_align_tmp_filename = prev_curr_align
                    self.curr_iter_tree_tmp_filename = prev_curr_tree 

                break_strategy_index += 1

                # self.status('current score: %s, best score: %s' % (self.score, self.best_score) )
                
            if not this_iter_score_improved:
                self.num_iter_since_imp += 1
            self.current_iteration += 1

        if self._termination_trigger:
            _LOG.debug("Termination trigger = %s" % self._termination_trigger)
        record_timestamp(os.path.join(tmp_dir_par, 'end_sateiter_timestamp.txt'))

        ### TODO: if configuration is 'return_final_iter_TreeAndAlignpair', then skip the following three lines
        if not self.return_final_tree_and_alignment:
            self.multilocus_dataset = self.best_multilocus_dataset.new_with_shared_meta()
            for locus_alignment in self.best_multilocus_dataset:
                self.multilocus_dataset.append(copy.copy(locus_alignment))
            self.tree_str = self.best_tree_str
            self.score = self.best_score
        else:
            assert self.multilocus_dataset is not None
            assert self.tree_str is not None
            assert self.score is not None
Example #9
0
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
Example #10
0
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)