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
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()
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
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
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
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()
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()
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
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)
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:
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
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
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
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
######
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)
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)
