def correct():
answers = request.form.getlist('question[]')
inputfile = request.files.get('file')
inputfile.save('input/' + inputfile.filename)
answers = [question for question in answers if question]
corrector.main(inputfile.filename, answers)
df = pd.read_csv('static/output.csv')
df.index += 1
return df.to_html()
def main(args):
os.environ["LC_ALL"] = "C"
if len(args) == 1:
options_storage.usage(spades_version)
sys.exit(0)
log = logging.getLogger('spades')
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.DEBUG)
log.addHandler(console)
support.check_binaries(bin_home, log)
# parse options and safe all parameters to cfg
cfg, dataset_data = fill_cfg(args, log)
if options_storage.continue_mode:
cmd_line, options = get_options_from_params(os.path.join(options_storage.output_dir, "params.txt"))
if not options:
support.error("failed to parse command line of the previous run! Please restart from the beginning or specify another output directory.")
cfg, dataset_data = fill_cfg(options, log)
if options_storage.restart_from:
check_cfg_for_restart_from(cfg)
options_storage.continue_mode = True
log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
if options_storage.continue_mode:
log_handler = logging.FileHandler(log_filename, mode='a')
else:
log_handler = logging.FileHandler(log_filename, mode='w')
log.addHandler(log_handler)
if options_storage.continue_mode:
log.info("\n======= SPAdes pipeline continued. Log can be found here: " + log_filename + "\n")
log.info("Restored from " + cmd_line)
if options_storage.restart_from:
updated_params = ""
flag = False
for v in args[1:]:
if v == '-o' or v == '--restart-from':
flag = True
continue
if flag:
flag = False
continue
updated_params += " " + v
updated_params = updated_params.strip()
log.info("with updated parameters: " + updated_params)
cmd_line += " " + updated_params
log.info("")
params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
params_handler = logging.FileHandler(params_filename, mode='w')
log.addHandler(params_handler)
if options_storage.continue_mode:
log.info(cmd_line)
else:
command = "Command line:"
for v in args:
command += " " + v
log.info(command)
# special case
if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(dataset_data, 'paired-end'):
support.warning('cannot perform mismatch correction without at least one paired-end library! Skipping this step.', log)
del cfg["mismatch_corrector"]
print_used_values(cfg, log)
log.removeHandler(params_handler)
if not options_storage.continue_mode:
log.info("\n======= SPAdes pipeline started. Log can be found here: " + log_filename + "\n")
# splitting interlaced reads and processing Ns in additional contigs if needed
if support.dataset_has_interlaced_reads(dataset_data) or support.dataset_has_additional_contigs(dataset_data):
dir_for_split_reads = os.path.join(options_storage.output_dir, 'split_input')
if support.dataset_has_interlaced_reads(dataset_data):
if not os.path.isdir(dir_for_split_reads):
os.makedirs(dir_for_split_reads)
dataset_data = support.split_interlaced_reads(dataset_data, dir_for_split_reads, log)
if support.dataset_has_additional_contigs(dataset_data):
dataset_data = support.process_Ns_in_additional_contigs(dataset_data, dir_for_split_reads, log)
options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
pyyaml.dump(dataset_data, open(options_storage.dataset_yaml_filename, 'w'))
cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename
try:
# copying configs before all computations (to prevent its changing at run time)
tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
if os.path.isdir(tmp_configs_dir) and not options_storage.continue_mode:
shutil.rmtree(tmp_configs_dir)
if not os.path.isdir(tmp_configs_dir):
dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False)
corrected_dataset_yaml_filename = ''
if "error_correction" in cfg:
STAGE_NAME = "Read error correction"
bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
corrected_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "corrected.yaml")
if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
and not options_storage.restart_from == "ec":
log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
else:
support.continue_from_here(log)
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in bh_cfg.__dict__:
os.environ["HEAPCHECK"] = bh_cfg.heap_check
if os.path.exists(bh_cfg.output_dir):
shutil.rmtree(bh_cfg.output_dir)
os.makedirs(bh_cfg.output_dir)
if support.get_lib_ids_by_type(dataset_data, options_storage.LONG_READS_TYPES):
not_used_dataset_data = support.get_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_data = support.rm_libs_by_type(dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "to_correct.yaml")
pyyaml.dump(to_correct_dataset_data, open(to_correct_dataset_yaml_filename, 'w'))
bh_cfg.__dict__["dataset_yaml_filename"] = to_correct_dataset_yaml_filename
else:
not_used_dataset_data = None
bh_cfg.__dict__["dataset_yaml_filename"] = cfg["dataset"].yaml_filename
log.info("\n===== %s started. \n" % STAGE_NAME)
hammer_logic.run_hammer(corrected_dataset_yaml_filename, tmp_configs_dir, bin_home, bh_cfg, not_used_dataset_data,
ext_python_modules_home, log)
log.info("\n===== %s finished. \n" % STAGE_NAME)
result_contigs_filename = os.path.join(cfg["common"].output_dir, "contigs.fasta")
result_scaffolds_filename = os.path.join(cfg["common"].output_dir, "scaffolds.fasta")
misc_dir = os.path.join(cfg["common"].output_dir, "misc")
### if mismatch correction is enabled then result contigs are copied to misc directory
assembled_contigs_filename = os.path.join(misc_dir, "assembled_contigs.fasta")
assembled_scaffolds_filename = os.path.join(misc_dir, "assembled_scaffolds.fasta")
if "assembly" in cfg:
STAGE_NAME = "Assembling"
spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
spades_cfg.__dict__["result_contigs"] = result_contigs_filename
spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
or ("mismatch_corrector" in cfg and
os.path.isfile(assembled_contigs_filename)))\
and not options_storage.restart_from == 'as' \
and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):
log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
# calculating latest_dir for the next stages
latest_dir = support.get_latest_dir(os.path.join(spades_cfg.output_dir, "K*"))
if not latest_dir:
support.error("failed to continue the previous run! Please restart from previous stages or from the beginning.", log)
else:
old_result_files = [result_contigs_filename, result_scaffolds_filename,
assembled_contigs_filename, assembled_scaffolds_filename]
for format in [".fasta", ".fastg"]:
for old_result_file in old_result_files:
if os.path.isfile(old_result_file[:-6] + format):
os.remove(old_result_file[:-6] + format)
if options_storage.restart_from == 'as':
support.continue_from_here(log)
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
if spades_cfg.disable_rr:
spades_cfg.__dict__["rr_enable"] = False
else:
spades_cfg.__dict__["rr_enable"] = True
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in spades_cfg.__dict__:
os.environ["HEAPCHECK"] = spades_cfg.heap_check
log.info("\n===== %s started.\n" % STAGE_NAME)
# creating dataset
dataset_filename = os.path.join(spades_cfg.output_dir, "dataset.info")
if not os.path.isfile(dataset_filename) or not options_storage.continue_mode:
dataset_file = open(dataset_filename, 'w')
import process_cfg
dataset_file.write("single_cell" + '\t' + process_cfg.bool_to_str(cfg["dataset"].single_cell) + '\n')
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_file.write("reads" + '\t' + process_cfg.process_spaces(corrected_dataset_yaml_filename) + '\n')
else:
dataset_file.write("reads" + '\t' + process_cfg.process_spaces(cfg["dataset"].yaml_filename) + '\n')
if spades_cfg.developer_mode and "reference" in cfg["dataset"].__dict__:
dataset_file.write("reference_genome" + '\t')
dataset_file.write(process_cfg.process_spaces(cfg["dataset"].reference) + '\n')
dataset_file.close()
spades_cfg.__dict__["dataset"] = dataset_filename
latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, dataset_data, ext_python_modules_home, log)
if os.path.isdir(misc_dir) and not options_storage.continue_mode:
shutil.rmtree(misc_dir)
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith('k'):
k_str = options_storage.restart_from[1:]
if k_str.find(":") != -1:
k_str = k_str[:k_str.find(":")]
support.error("failed to continue from K=%s because this K was not processed in the original run!" % k_str, log)
log.info("\n===== %s finished. \n" % STAGE_NAME)
#corrector
if "mismatch_corrector" in cfg and (os.path.isfile(result_contigs_filename) or
(options_storage.continue_mode and os.path.isfile(assembled_contigs_filename))):
STAGE_NAME = "Mismatch correction"
to_correct = dict()
to_correct["contigs"] = (result_contigs_filename, assembled_contigs_filename)
if os.path.isfile(result_scaffolds_filename) or (options_storage.continue_mode and
os.path.isfile(assembled_scaffolds_filename)):
to_correct["scaffolds"] = (result_scaffolds_filename, assembled_scaffolds_filename)
# moving assembled contigs (scaffolds) to misc dir
for assembly_type, (old, new) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(new):
continue
for format in [".fasta", ".fastg"]:
if os.path.isfile(old[:-6] + format):
shutil.move(old[:-6] + format, new[:-6] + format)
if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
(os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
and not options_storage.restart_from == 'mc':
log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)
else:
if options_storage.restart_from == 'mc':
support.continue_from_here(log)
log.info("\n===== %s started." % STAGE_NAME)
# detecting paired-end library with the largest insert size
est_params_data = pyyaml.load(open(os.path.join(latest_dir, "final.lib_data"), 'r'))
max_IS_library = None
for reads_library in est_params_data:
if reads_library['type'] == 'paired-end':
if not max_IS_library or float(reads_library["insert size mean"]) > float(max_IS_library["insert size mean"]):
max_IS_library = reads_library
if not max_IS_library:
support.error('Mismatch correction cannot be performed without at least one paired-end library!', log)
if not max_IS_library["insert size mean"]:
support.warning('Failed to estimate insert size for all paired-end libraries. Starting Mismatch correction'
' based on the first paired-end library and with default insert size.', log)
else:
cfg["mismatch_corrector"].__dict__["insert-size"] = round(max_IS_library["insert size mean"])
yaml_dirname = os.path.dirname(options_storage.dataset_yaml_filename)
cfg["mismatch_corrector"].__dict__["1"] = list(map(lambda x: os.path.join(yaml_dirname, x),
max_IS_library['left reads']))
cfg["mismatch_corrector"].__dict__["2"] = list(map(lambda x: os.path.join(yaml_dirname, x),
max_IS_library['right reads']))
#TODO: add reads orientation
import corrector
corrector_cfg = cfg["mismatch_corrector"]
args = []
for key, values in corrector_cfg.__dict__.items():
if key == "output-dir":
continue
# for processing list of reads
if not isinstance(values, list):
values = [values]
for value in values:
if len(key) == 1:
args.append('-' + key)
else:
args.append('--' + key)
if value is not None:
args.append(value)
# processing contigs and scaffolds (or only contigs)
for assembly_type, (corrected, assembled) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(corrected):
log.info("\n== Skipping processing of " + assembly_type + " (already processed)\n")
continue
support.continue_from_here(log)
log.info("\n== Processing of " + assembly_type + "\n")
cur_args = args[:]
cur_args += ['-c', assembled]
tmp_dir_for_corrector = support.get_tmp_dir(prefix="mis_cor_%s_" % assembly_type)
cur_args += ['--output-dir', tmp_dir_for_corrector]
# correcting
corrector.main(cur_args, ext_python_modules_home, log)
result_corrected_filename = os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta")
# moving corrected contigs (scaffolds) to SPAdes output dir
if os.path.isfile(result_corrected_filename):
shutil.move(result_corrected_filename, corrected)
if os.path.isdir(tmp_dir_for_corrector):
shutil.rmtree(tmp_dir_for_corrector)
assembled_fastg = assembled[:-6] + ".fastg"
if os.path.isfile(assembled_fastg):
support.create_fastg_from_fasta(corrected, assembled_fastg, log)
log.info("\n===== %s finished.\n" % STAGE_NAME)
if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
shutil.rmtree(tmp_configs_dir)
#log.info("")
if "error_correction" in cfg and os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
log.info(" * Corrected reads are in " + support.process_spaces(os.path.dirname(corrected_dataset_yaml_filename) + "/"))
if "assembly" in cfg and os.path.isfile(result_contigs_filename):
message = " * Assembled contigs are in " + support.process_spaces(result_contigs_filename)
if os.path.isfile(result_contigs_filename[:-6] + ".fastg"):
message += " (" + os.path.basename(result_contigs_filename[:-6] + ".fastg") + ")"
log.info(message)
if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
message = " * Assembled scaffolds are in " + support.process_spaces(result_scaffolds_filename)
if os.path.isfile(result_scaffolds_filename[:-6] + ".fastg"):
message += " (" + os.path.basename(result_scaffolds_filename[:-6] + ".fastg") + ")"
log.info(message)
#log.info("")
#breaking scaffolds
if os.path.isfile(result_scaffolds_filename):
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
result_broken_scaffolds = os.path.join(misc_dir, "broken_scaffolds.fasta")
if not os.path.isfile(result_broken_scaffolds) or not options_storage.continue_mode:
modified, broken_scaffolds = support.break_scaffolds(result_scaffolds_filename,
options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
if modified:
support.write_fasta(result_broken_scaffolds, broken_scaffolds)
#log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
# " Ns are in " + result_broken_scaffolds)
### printing WARNINGS SUMMARY
if not support.log_warnings(log):
log.info("\n======= SPAdes pipeline finished.") # otherwise it finished WITH WARNINGS
if options_storage.test_mode:
for result_filename in [result_contigs_filename, result_scaffolds_filename]:
if os.path.isfile(result_filename):
result_fasta = list(support.read_fasta(result_filename))
# correctness check: should be one contig of length 1000 bp
correct_number = 1
correct_length = 1000
if not len(result_fasta):
support.error("TEST FAILED: %s does not contain contigs!" % result_filename)
elif len(result_fasta) > correct_number:
support.error("TEST FAILED: %s contains more than %d contig (%d)!" %
(result_filename, correct_number, len(result_fasta)))
elif len(result_fasta[0][1]) != correct_length:
if len(result_fasta[0][1]) > correct_length:
relation = "more"
else:
relation = "less"
support.error("TEST FAILED: %s contains %s than %d bp (%d bp)!" %
(result_filename, relation, correct_length, len(result_fasta[0][1])))
else:
support.error("TEST FAILED: " + result_filename + " does not exist!")
log.info("\n========= TEST PASSED CORRECTLY.")
log.info("\nSPAdes log can be found here: " + log_filename)
log.info("")
log.info("Thank you for using SPAdes!")
log.removeHandler(log_handler)
except Exception:
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
if exc_type == OSError and exc_value.errno == errno.ENOEXEC: # Exec format error
support.error("It looks like you are using SPAdes binaries for another platform.\n" +
support.get_spades_binaries_info_message())
else:
log.exception(exc_value)
support.error("exception caught: %s" % exc_type, log)
except BaseException: # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
log.exception(exc_value)
support.error("exception caught: %s" % exc_type, log)
def main():
os.environ["LC_ALL"] = "C"
if len(sys.argv) == 1:
options_storage.usage(spades_version)
sys.exit(0)
log = logging.getLogger('spades')
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.DEBUG)
log.addHandler(console)
check_binaries(bin_home, log)
# parse options and safe all parameters to cfg
cfg, dataset_data = fill_cfg(sys.argv, log)
if options_storage.continue_mode:
cmd_line, options = get_options_from_params(
os.path.join(options_storage.output_dir, "params.txt"))
if not options:
support.error(
"failed to parse command line of the previous run! Please restart from the beginning."
)
cfg, dataset_data = fill_cfg(options, log)
options_storage.continue_mode = True
log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
if options_storage.continue_mode:
log_handler = logging.FileHandler(log_filename, mode='a')
else:
log_handler = logging.FileHandler(log_filename, mode='w')
log.addHandler(log_handler)
if options_storage.continue_mode:
log.info(
"\n======= SPAdes pipeline continued. Log can be found here: " +
log_filename + "\n")
log.info("Restored from " + cmd_line)
else:
params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
params_handler = logging.FileHandler(params_filename, mode='w')
log.addHandler(params_handler)
command = "Command line:"
for v in sys.argv:
command += " " + v
log.info(command)
print_used_values(cfg, log)
log.removeHandler(params_handler)
log.info("\n======= SPAdes pipeline started. Log can be found here: " +
log_filename + "\n")
# splitting interlaced reads if needed
if support.dataset_has_interlaced_reads(dataset_data):
dir_for_split_reads = os.path.join(
os.path.abspath(options_storage.output_dir), 'split_reads')
if not os.path.isdir(dir_for_split_reads):
os.makedirs(dir_for_split_reads)
dataset_data = support.split_interlaced_reads(dataset_data,
dir_for_split_reads, log)
options_storage.dataset_yaml_filename = os.path.join(
options_storage.output_dir, "input_dataset.yaml")
pyyaml.dump(dataset_data,
open(options_storage.dataset_yaml_filename, 'w'))
cfg["dataset"].yaml_filename = os.path.abspath(
options_storage.dataset_yaml_filename)
try:
# copying configs before all computations (to prevent its changing at run time)
tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
if os.path.isdir(
tmp_configs_dir) and not options_storage.continue_mode:
shutil.rmtree(tmp_configs_dir)
if not os.path.isdir(tmp_configs_dir):
shutil.copytree(os.path.join(spades_home, "configs"),
tmp_configs_dir)
corrected_dataset_yaml_filename = ''
if "error_correction" in cfg:
bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
bh_cfg.__dict__["dataset_yaml_filename"] = cfg[
"dataset"].yaml_filename
corrected_dataset_yaml_filename = os.path.join(
bh_cfg.output_dir, "corrected.yaml")
if os.path.isfile(corrected_dataset_yaml_filename
) and options_storage.continue_mode:
log.info(
"\n===== Skipping read error correction (already processed). \n"
)
else:
options_storage.continue_mode = False # continue from here
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in bh_cfg.__dict__:
os.environ["HEAPCHECK"] = bh_cfg.heap_check
if os.path.exists(bh_cfg.output_dir):
shutil.rmtree(bh_cfg.output_dir)
os.makedirs(bh_cfg.output_dir)
if not os.path.exists(bh_cfg.tmp_dir):
os.makedirs(bh_cfg.tmp_dir)
log.info("\n===== Read error correction started. \n")
bh_logic.run_bh(corrected_dataset_yaml_filename,
tmp_configs_dir, bin_home, bh_cfg,
ext_python_modules_home, log)
log.info("\n===== Read error correction finished. \n")
result_contigs_filename = os.path.join(cfg["common"].output_dir,
"contigs.fasta")
result_scaffolds_filename = os.path.join(cfg["common"].output_dir,
"scaffolds.fasta")
misc_dir = os.path.join(cfg["common"].output_dir, "misc")
### if mismatch correction is enabled then result contigs are copied to misc directory
assembled_contigs_filename = os.path.join(misc_dir,
"assembled_contigs.fasta")
assembled_scaffolds_filename = os.path.join(
misc_dir, "assembled_scaffolds.fasta")
if "assembly" in cfg:
spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
spades_cfg.__dict__["result_contigs"] = result_contigs_filename
spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
spades_cfg.__dict__["additional_contigs"] = os.path.join(
spades_cfg.output_dir, "simplified_contigs.fasta")
if options_storage.continue_mode and (
os.path.isfile(spades_cfg.result_contigs) or
("mismatch_corrector" in cfg
and os.path.isfile(assembled_contigs_filename))):
log.info("\n===== Skipping assembling (already processed). \n")
# calculating latest_dir for the next stages
latest_dir = support.get_latest_dir(
os.path.join(spades_cfg.output_dir, "K*"))
if not latest_dir:
support.error(
"failed to continue the previous run! Please restart from the beginning."
)
else:
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_data = pyyaml.load(
open(corrected_dataset_yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(
dataset_data,
os.path.dirname(corrected_dataset_yaml_filename))
if support.dataset_has_paired_reads(dataset_data):
spades_cfg.__dict__["paired_mode"] = True
else:
spades_cfg.__dict__["paired_mode"] = False
if options_storage.rectangles:
spades_cfg.__dict__["resolving_mode"] = "rectangles"
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in spades_cfg.__dict__:
os.environ["HEAPCHECK"] = spades_cfg.heap_check
log.info("\n===== Assembling started.\n")
# creating dataset
dataset_filename = os.path.join(spades_cfg.output_dir,
"dataset.info")
if not os.path.isfile(
dataset_filename) or not options_storage.continue_mode:
dataset_file = open(dataset_filename, 'w')
import process_cfg
dataset_file.write(
"single_cell" + '\t' +
process_cfg.bool_to_str(cfg["dataset"].single_cell) +
'\n')
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_file.write(
"reads" + '\t' + process_cfg.process_spaces(
corrected_dataset_yaml_filename) + '\n')
else:
dataset_file.write("reads" + '\t' +
process_cfg.process_spaces(
cfg["dataset"].yaml_filename) +
'\n')
if spades_cfg.developer_mode and "reference" in cfg[
"dataset"].__dict__:
dataset_file.write("reference_genome" + '\t')
dataset_file.write(
process_cfg.process_spaces(
os.path.abspath(cfg["dataset"].reference)) +
'\n')
dataset_file.close()
spades_cfg.__dict__["dataset"] = dataset_filename
latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home,
spades_cfg, log)
#rectangles
if spades_cfg.paired_mode and options_storage.rectangles:
if options_storage.continue_mode: # TODO: continue mode
support.warning(
"sorry, --continue doesn't work with --rectangles yet. Skipping repeat resolving."
)
else:
sys.path.append(
os.path.join(python_modules_home, "rectangles"))
import rrr
rrr_input_dir = os.path.join(latest_dir, "saves")
rrr_outpath = os.path.join(spades_cfg.output_dir,
"rectangles")
if not os.path.exists(rrr_outpath):
os.mkdir(rrr_outpath)
rrr_reference_information_file = os.path.join(
rrr_input_dir,
"late_pair_info_counted_etalon_distance.txt")
rrr_test_util = rrr.TestUtils(
rrr_reference_information_file,
os.path.join(rrr_outpath, "rectangles.log"))
rrr.resolve(rrr_input_dir, rrr_outpath, rrr_test_util,
"", cfg["dataset"].single_cell,
spades_cfg.careful)
shutil.copyfile(
os.path.join(
rrr_outpath,
"rectangles_extend_before_scaffold.fasta"),
spades_cfg.result_contigs)
shutil.copyfile(
os.path.join(rrr_outpath,
"rectangles_extend.fasta"),
spades_cfg.result_scaffolds)
if not spades_cfg.developer_mode:
if os.path.exists(rrr_input_dir):
shutil.rmtree(rrr_input_dir)
if os.path.exists(rrr_outpath):
shutil.rmtree(rrr_outpath, True)
if os.path.exists(rrr_outpath):
os.system('rm -r ' + rrr_outpath)
#EOR
if os.path.isdir(
misc_dir) and not options_storage.continue_mode:
shutil.rmtree(misc_dir)
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
if os.path.isfile(spades_cfg.additional_contigs):
shutil.move(spades_cfg.additional_contigs, misc_dir)
log.info("\n===== Assembling finished. \n")
#corrector
if "mismatch_corrector" in cfg and (
os.path.isfile(result_contigs_filename) or
(options_storage.continue_mode
and os.path.isfile(assembled_contigs_filename))):
to_correct = dict()
to_correct["contigs"] = (result_contigs_filename,
assembled_contigs_filename)
if os.path.isfile(result_scaffolds_filename) or (
options_storage.continue_mode
and os.path.isfile(assembled_scaffolds_filename)):
to_correct["scaffolds"] = (result_scaffolds_filename,
assembled_scaffolds_filename)
# moving assembled contigs (scaffolds) to misc dir
for k, (old, new) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(new):
continue
shutil.move(old, new)
if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
(os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)):
log.info(
"\n===== Skipping mismatch correction (already processed). \n"
)
else:
log.info("\n===== Mismatch correction started.")
# detecting paired-end library with the largest insert size
dataset_data = pyyaml.load(
open(options_storage.dataset_yaml_filename, 'r')
) ### initial dataset, i.e. before error correction
dataset_data = support.relative2abs_paths(
dataset_data,
os.path.dirname(options_storage.dataset_yaml_filename))
paired_end_libraries_ids = []
for id, reads_library in enumerate(dataset_data):
if reads_library['type'] == 'paired-end':
paired_end_libraries_ids.append(id)
if not len(paired_end_libraries_ids):
support.error(
'Mismatch correction cannot be performed without at least one paired-end library!'
)
estimated_params = load_config_from_file(
os.path.join(latest_dir, "_est_params.info"))
max_insert_size = -1
target_paired_end_library_id = -1
for id in paired_end_libraries_ids:
if float(estimated_params.__dict__[
"insert_size_" + str(id)]) > max_insert_size:
max_insert_size = float(
estimated_params.__dict__["insert_size_" +
str(id)])
target_paired_end_library_id = id
yaml_dirname = os.path.dirname(
options_storage.dataset_yaml_filename)
cfg["mismatch_corrector"].__dict__["1"] = list(
map(
lambda x: os.path.join(yaml_dirname, x),
dataset_data[target_paired_end_library_id]
['left reads']))
cfg["mismatch_corrector"].__dict__["2"] = list(
map(
lambda x: os.path.join(yaml_dirname, x),
dataset_data[target_paired_end_library_id]
['right reads']))
cfg["mismatch_corrector"].__dict__["insert-size"] = round(
max_insert_size)
#TODO: add reads orientation
import corrector
corrector_cfg = cfg["mismatch_corrector"]
args = []
for key, values in corrector_cfg.__dict__.items():
if key == "output-dir":
continue
# for processing list of reads
if not isinstance(values, list):
values = [values]
for value in values:
if len(key) == 1:
args.append('-' + key)
else:
args.append('--' + key)
if value:
args.append(value)
# processing contigs and scaffolds (or only contigs)
for k, (corrected, assembled) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(
corrected):
log.info("\n== Skipping processing of " + k +
" (already processed)\n")
continue
options_storage.continue_mode = False
log.info("\n== Processing of " + k + "\n")
cur_args = args[:]
cur_args += ['-c', assembled]
tmp_dir_for_corrector = os.path.join(
corrector_cfg.__dict__["output-dir"],
"mismatch_corrector_" + k)
cur_args += ['--output-dir', tmp_dir_for_corrector]
# correcting
corrector.main(cur_args, ext_python_modules_home, log)
result_corrected_filename = os.path.abspath(
os.path.join(tmp_dir_for_corrector,
"corrected_contigs.fasta"))
# moving corrected contigs (scaffolds) to SPAdes output dir
if os.path.isfile(result_corrected_filename):
shutil.move(result_corrected_filename, corrected)
if os.path.isdir(tmp_dir_for_corrector):
shutil.rmtree(tmp_dir_for_corrector)
log.info("\n===== Mismatch correction finished.\n")
if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
shutil.rmtree(tmp_configs_dir)
#log.info("")
if os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
log.info(" * Corrected reads are in " +
os.path.dirname(corrected_dataset_yaml_filename) + "/")
if os.path.isfile(result_contigs_filename):
log.info(" * Assembled contigs are in " + result_contigs_filename)
if os.path.isfile(result_scaffolds_filename):
log.info(" * Assembled scaffolds are in " +
result_scaffolds_filename)
#log.info("")
#breaking scaffolds
if os.path.isfile(result_scaffolds_filename):
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
result_broken_scaffolds = os.path.join(misc_dir,
"broken_scaffolds.fasta")
threshold = 3
if not os.path.isfile(result_broken_scaffolds
) or not options_storage.continue_mode:
support.break_scaffolds(result_scaffolds_filename, threshold,
result_broken_scaffolds)
#log.info(" * Scaffolds broken by " + str(threshold) + " Ns are in " + result_broken_scaffolds)
### printing WARNINGS SUMMARY
if not support.log_warnings(log):
log.info("\n======= SPAdes pipeline finished."
) # otherwise it finished WITH WARNINGS
log.info("\nSPAdes log can be found here: " + log_filename)
log.info("")
log.info("Thank you for using SPAdes!")
log.removeHandler(log_handler)
except Exception:
_, exc, _ = sys.exc_info()
log.exception(exc)
support.error("exception caught", log)
def main(args):
os.environ["LC_ALL"] = "C"
if len(args) == 1:
options_storage.usage(spades_version)
sys.exit(0)
log = logging.getLogger('spades')
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.DEBUG)
log.addHandler(console)
support.check_binaries(bin_home, log)
# parse options and safe all parameters to cfg
options = args
cfg, dataset_data = fill_cfg(options, log)
if options_storage.continue_mode:
cmd_line, options = get_options_from_params(
os.path.join(options_storage.output_dir, "params.txt"), args[0])
if not options:
support.error(
"failed to parse command line of the previous run! Please restart from the beginning or specify another output directory."
)
cfg, dataset_data = fill_cfg(options, log)
if options_storage.restart_from:
check_cfg_for_restart_from(cfg)
options_storage.continue_mode = True
log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
if options_storage.continue_mode:
log_handler = logging.FileHandler(log_filename, mode='a')
else:
log_handler = logging.FileHandler(log_filename, mode='w')
log.addHandler(log_handler)
if options_storage.continue_mode:
log.info(
"\n======= SPAdes pipeline continued. Log can be found here: " +
log_filename + "\n")
log.info("Restored from " + cmd_line)
if options_storage.restart_from:
updated_params = ""
flag = False
for v in args[1:]:
if v == '-o' or v == '--restart-from':
flag = True
continue
if flag:
flag = False
continue
updated_params += " " + v
updated_params = updated_params.strip()
log.info("with updated parameters: " + updated_params)
cmd_line += " " + updated_params
log.info("")
params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
params_handler = logging.FileHandler(params_filename, mode='w')
log.addHandler(params_handler)
if options_storage.continue_mode:
log.info(cmd_line)
else:
command = "Command line:"
for v in args:
command += " " + v
log.info(command)
# special case
if "mismatch_corrector" in cfg and not support.get_lib_ids_by_type(
dataset_data, 'paired-end'):
support.warning(
'cannot perform mismatch correction without at least one paired-end library! Skipping this step.',
log)
del cfg["mismatch_corrector"]
print_used_values(cfg, log)
log.removeHandler(params_handler)
support.check_single_reads_in_options(options, log)
if not options_storage.continue_mode:
log.info("\n======= SPAdes pipeline started. Log can be found here: " +
log_filename + "\n")
# splitting interlaced reads and processing Ns in additional contigs if needed
if support.dataset_has_interlaced_reads(
dataset_data) or support.dataset_has_additional_contigs(
dataset_data):
dir_for_split_reads = os.path.join(options_storage.output_dir,
'split_input')
if support.dataset_has_interlaced_reads(dataset_data):
if not os.path.isdir(dir_for_split_reads):
os.makedirs(dir_for_split_reads)
dataset_data = support.split_interlaced_reads(
dataset_data, dir_for_split_reads, log)
if support.dataset_has_additional_contigs(dataset_data):
dataset_data = support.process_Ns_in_additional_contigs(
dataset_data, dir_for_split_reads, log)
options_storage.dataset_yaml_filename = os.path.join(
options_storage.output_dir, "input_dataset.yaml")
pyyaml.dump(dataset_data,
open(options_storage.dataset_yaml_filename, 'w'))
cfg["dataset"].yaml_filename = options_storage.dataset_yaml_filename
try:
# copying configs before all computations (to prevent its changing at run time)
tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
if os.path.isdir(
tmp_configs_dir) and not options_storage.continue_mode:
shutil.rmtree(tmp_configs_dir)
if not os.path.isdir(tmp_configs_dir):
dir_util.copy_tree(os.path.join(spades_home, "configs"),
tmp_configs_dir,
preserve_times=False)
corrected_dataset_yaml_filename = ''
if "error_correction" in cfg:
STAGE_NAME = "Read error correction"
bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
corrected_dataset_yaml_filename = os.path.join(
bh_cfg.output_dir, "corrected.yaml")
if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \
and not options_storage.restart_from == "ec":
log.info("\n===== Skipping %s (already processed). \n" %
STAGE_NAME)
else:
support.continue_from_here(log)
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in bh_cfg.__dict__:
os.environ["HEAPCHECK"] = bh_cfg.heap_check
if os.path.exists(bh_cfg.output_dir):
shutil.rmtree(bh_cfg.output_dir)
os.makedirs(bh_cfg.output_dir)
if support.get_lib_ids_by_type(
dataset_data, options_storage.LONG_READS_TYPES):
not_used_dataset_data = support.get_libs_by_type(
dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_data = support.rm_libs_by_type(
dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_yaml_filename = os.path.join(
bh_cfg.output_dir, "to_correct.yaml")
pyyaml.dump(to_correct_dataset_data,
open(to_correct_dataset_yaml_filename, 'w'))
bh_cfg.__dict__[
"dataset_yaml_filename"] = to_correct_dataset_yaml_filename
else:
not_used_dataset_data = None
bh_cfg.__dict__["dataset_yaml_filename"] = cfg[
"dataset"].yaml_filename
log.info("\n===== %s started. \n" % STAGE_NAME)
hammer_logic.run_hammer(corrected_dataset_yaml_filename,
tmp_configs_dir, bin_home, bh_cfg,
not_used_dataset_data,
ext_python_modules_home, log)
log.info("\n===== %s finished. \n" % STAGE_NAME)
result_contigs_filename = os.path.join(cfg["common"].output_dir,
"contigs.fasta")
result_scaffolds_filename = os.path.join(cfg["common"].output_dir,
"scaffolds.fasta")
misc_dir = os.path.join(cfg["common"].output_dir, "misc")
### if mismatch correction is enabled then result contigs are copied to misc directory
assembled_contigs_filename = os.path.join(misc_dir,
"assembled_contigs.fasta")
assembled_scaffolds_filename = os.path.join(
misc_dir, "assembled_scaffolds.fasta")
if "assembly" in cfg:
STAGE_NAME = "Assembling"
spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
spades_cfg.__dict__["result_contigs"] = result_contigs_filename
spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
or ("mismatch_corrector" in cfg and
os.path.isfile(assembled_contigs_filename)))\
and not options_storage.restart_from == 'as' \
and not (options_storage.restart_from and options_storage.restart_from.startswith('k')):
log.info("\n===== Skipping %s (already processed). \n" %
STAGE_NAME)
# calculating latest_dir for the next stages
latest_dir = support.get_latest_dir(
os.path.join(spades_cfg.output_dir, "K*"))
if not latest_dir:
support.error(
"failed to continue the previous run! Please restart from previous stages or from the beginning.",
log)
else:
old_result_files = [
result_contigs_filename, result_scaffolds_filename,
assembled_contigs_filename, assembled_scaffolds_filename
]
for format in [".fasta", ".fastg"]:
for old_result_file in old_result_files:
if os.path.isfile(old_result_file[:-6] + format):
os.remove(old_result_file[:-6] + format)
if options_storage.restart_from == 'as':
support.continue_from_here(log)
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_data = pyyaml.load(
open(corrected_dataset_yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(
dataset_data,
os.path.dirname(corrected_dataset_yaml_filename))
if spades_cfg.disable_rr:
spades_cfg.__dict__["rr_enable"] = False
else:
spades_cfg.__dict__["rr_enable"] = True
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in spades_cfg.__dict__:
os.environ["HEAPCHECK"] = spades_cfg.heap_check
log.info("\n===== %s started.\n" % STAGE_NAME)
# creating dataset
dataset_filename = os.path.join(spades_cfg.output_dir,
"dataset.info")
if not os.path.isfile(
dataset_filename) or not options_storage.continue_mode:
dataset_file = open(dataset_filename, 'w')
import process_cfg
dataset_file.write(
"single_cell" + '\t' +
process_cfg.bool_to_str(cfg["dataset"].single_cell) +
'\n')
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_file.write(
"reads" + '\t' + process_cfg.process_spaces(
corrected_dataset_yaml_filename) + '\n')
else:
dataset_file.write("reads" + '\t' +
process_cfg.process_spaces(
cfg["dataset"].yaml_filename) +
'\n')
if spades_cfg.developer_mode and "reference" in cfg[
"dataset"].__dict__:
dataset_file.write("reference_genome" + '\t')
dataset_file.write(
process_cfg.process_spaces(
cfg["dataset"].reference) + '\n')
dataset_file.close()
spades_cfg.__dict__["dataset"] = dataset_filename
latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home,
spades_cfg, dataset_data,
ext_python_modules_home,
log)
if os.path.isdir(
misc_dir) and not options_storage.continue_mode:
shutil.rmtree(misc_dir)
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
if options_storage.continue_mode and options_storage.restart_from and options_storage.restart_from.startswith(
'k'):
k_str = options_storage.restart_from[1:]
if k_str.find(":") != -1:
k_str = k_str[:k_str.find(":")]
support.error(
"failed to continue from K=%s because this K was not processed in the original run!"
% k_str, log)
log.info("\n===== %s finished. \n" % STAGE_NAME)
#corrector
if "mismatch_corrector" in cfg and (
os.path.isfile(result_contigs_filename) or
(options_storage.continue_mode
and os.path.isfile(assembled_contigs_filename))):
STAGE_NAME = "Mismatch correction"
to_correct = dict()
to_correct["contigs"] = (result_contigs_filename,
assembled_contigs_filename)
if os.path.isfile(result_scaffolds_filename) or (
options_storage.continue_mode
and os.path.isfile(assembled_scaffolds_filename)):
to_correct["scaffolds"] = (result_scaffolds_filename,
assembled_scaffolds_filename)
# moving assembled contigs (scaffolds) to misc dir
for assembly_type, (old, new) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(new):
continue
for format in [".fasta", ".fastg"]:
if os.path.isfile(old[:-6] + format):
shutil.move(old[:-6] + format, new[:-6] + format)
if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
(os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)) \
and not options_storage.restart_from == 'mc':
log.info("\n===== Skipping %s (already processed). \n" %
STAGE_NAME)
else:
if options_storage.restart_from == 'mc':
support.continue_from_here(log)
log.info("\n===== %s started." % STAGE_NAME)
# detecting paired-end library with the largest insert size
est_params_data = pyyaml.load(
open(os.path.join(latest_dir, "final.lib_data"), 'r'))
max_IS_library = None
for reads_library in est_params_data:
if reads_library['type'] == 'paired-end':
if not max_IS_library or float(
reads_library["insert size mean"]) > float(
max_IS_library["insert size mean"]):
max_IS_library = reads_library
if not max_IS_library:
support.error(
'Mismatch correction cannot be performed without at least one paired-end library!',
log)
if not max_IS_library["insert size mean"]:
support.warning(
'Failed to estimate insert size for all paired-end libraries. Starting Mismatch correction'
' based on the first paired-end library and with default insert size.',
log)
else:
cfg["mismatch_corrector"].__dict__[
"insert-size"] = round(
max_IS_library["insert size mean"])
yaml_dirname = os.path.dirname(
options_storage.dataset_yaml_filename)
cfg["mismatch_corrector"].__dict__["1"] = list(
map(lambda x: os.path.join(yaml_dirname, x),
max_IS_library['left reads']))
cfg["mismatch_corrector"].__dict__["2"] = list(
map(lambda x: os.path.join(yaml_dirname, x),
max_IS_library['right reads']))
#TODO: add reads orientation
import corrector
corrector_cfg = cfg["mismatch_corrector"]
args = []
for key, values in corrector_cfg.__dict__.items():
if key == "output-dir":
continue
# for processing list of reads
if not isinstance(values, list):
values = [values]
for value in values:
if len(key) == 1:
args.append('-' + key)
else:
args.append('--' + key)
if value is not None:
args.append(value)
# processing contigs and scaffolds (or only contigs)
for assembly_type, (corrected,
assembled) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(
corrected):
log.info("\n== Skipping processing of " +
assembly_type + " (already processed)\n")
continue
support.continue_from_here(log)
log.info("\n== Processing of " + assembly_type + "\n")
cur_args = args[:]
cur_args += ['-c', assembled]
tmp_dir_for_corrector = support.get_tmp_dir(
prefix="mis_cor_%s_" % assembly_type)
cur_args += ['--output-dir', tmp_dir_for_corrector]
# correcting
corrector.main(cur_args, ext_python_modules_home, log)
result_corrected_filename = os.path.join(
tmp_dir_for_corrector, "corrected_contigs.fasta")
# moving corrected contigs (scaffolds) to SPAdes output dir
if os.path.isfile(result_corrected_filename):
shutil.move(result_corrected_filename, corrected)
if os.path.isdir(tmp_dir_for_corrector):
shutil.rmtree(tmp_dir_for_corrector)
assembled_fastg = assembled[:-6] + ".fastg"
if os.path.isfile(assembled_fastg):
support.create_fastg_from_fasta(
corrected, assembled_fastg, log)
log.info("\n===== %s finished.\n" % STAGE_NAME)
if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
shutil.rmtree(tmp_configs_dir)
#log.info("")
if "error_correction" in cfg and os.path.isdir(
os.path.dirname(corrected_dataset_yaml_filename)):
log.info(" * Corrected reads are in " + support.process_spaces(
os.path.dirname(corrected_dataset_yaml_filename) + "/"))
if "assembly" in cfg and os.path.isfile(result_contigs_filename):
message = " * Assembled contigs are in " + support.process_spaces(
result_contigs_filename)
if os.path.isfile(result_contigs_filename[:-6] + ".fastg"):
message += " (" + os.path.basename(
result_contigs_filename[:-6] + ".fastg") + ")"
log.info(message)
if "assembly" in cfg and os.path.isfile(result_scaffolds_filename):
message = " * Assembled scaffolds are in " + support.process_spaces(
result_scaffolds_filename)
if os.path.isfile(result_scaffolds_filename[:-6] + ".fastg"):
message += " (" + os.path.basename(
result_scaffolds_filename[:-6] + ".fastg") + ")"
log.info(message)
#log.info("")
#breaking scaffolds
if os.path.isfile(result_scaffolds_filename):
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
result_broken_scaffolds = os.path.join(misc_dir,
"broken_scaffolds.fasta")
if not os.path.isfile(result_broken_scaffolds
) or not options_storage.continue_mode:
modified, broken_scaffolds = support.break_scaffolds(
result_scaffolds_filename,
options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)
if modified:
support.write_fasta(result_broken_scaffolds,
broken_scaffolds)
#log.info(" * Scaffolds broken by " + str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS) +
# " Ns are in " + result_broken_scaffolds)
### printing WARNINGS SUMMARY
if not support.log_warnings(log):
log.info("\n======= SPAdes pipeline finished."
) # otherwise it finished WITH WARNINGS
if options_storage.test_mode:
for result_filename in [
result_contigs_filename, result_scaffolds_filename
]:
if os.path.isfile(result_filename):
result_fasta = list(support.read_fasta(result_filename))
# correctness check: should be one contig of length 1000 bp
correct_number = 1
correct_length = 1000
if not len(result_fasta):
support.error(
"TEST FAILED: %s does not contain contigs!" %
result_filename)
elif len(result_fasta) > correct_number:
support.error(
"TEST FAILED: %s contains more than %d contig (%d)!"
% (result_filename, correct_number,
len(result_fasta)))
elif len(result_fasta[0][1]) != correct_length:
if len(result_fasta[0][1]) > correct_length:
relation = "more"
else:
relation = "less"
support.error(
"TEST FAILED: %s contains %s than %d bp (%d bp)!" %
(result_filename, relation, correct_length,
len(result_fasta[0][1])))
else:
support.error("TEST FAILED: " + result_filename +
" does not exist!")
log.info("\n========= TEST PASSED CORRECTLY.")
log.info("\nSPAdes log can be found here: " + log_filename)
log.info("")
log.info("Thank you for using SPAdes!")
log.removeHandler(log_handler)
except Exception:
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
if exc_type == OSError and exc_value.errno == errno.ENOEXEC: # Exec format error
support.error(
"It looks like you are using SPAdes binaries for another platform.\n"
+ support.get_spades_binaries_info_message())
else:
log.exception(exc_value)
support.error("exception caught: %s" % exc_type, log)
except BaseException: # since python 2.5 system-exiting exceptions (e.g. KeyboardInterrupt) are derived from BaseException
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
log.exception(exc_value)
support.error("exception caught: %s" % exc_type, log)
if value:
args.append(value)
# processing contigs and scaffolds (or only contigs)
for k, (corrected, assembled) in to_correct.items():
log.info("\n== Processing " + k + "\n")
cur_args = args[:]
cur_args += ["-c", assembled]
tmp_dir_for_corrector = os.path.join(
corrector_cfg.__dict__["output-dir"], "mismatch_corrector_" + k
)
cur_args += ["--output-dir", tmp_dir_for_corrector]
# correcting
corrector.main(cur_args, ext_python_modules_home, log)
result_corrected_filename = os.path.abspath(
os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta")
)
# moving corrected contigs (scaffolds) to SPAdes output dir
if os.path.isfile(result_corrected_filename):
shutil.move(result_corrected_filename, corrected)
if os.path.isdir(tmp_dir_for_corrector):
shutil.rmtree(tmp_dir_for_corrector)
log.info("\n===== Mismatch correction finished.\n")
if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
shutil.rmtree(tmp_configs_dir)
def main():
os.environ["LC_ALL"] = "C"
if len(sys.argv) == 1:
options_storage.usage(spades_version)
sys.exit(0)
log = logging.getLogger('spades')
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter('%(message)s'))
console.setLevel(logging.DEBUG)
log.addHandler(console)
check_binaries(bin_home, log)
# parse options and safe all parameters to cfg
cfg, dataset_data = fill_cfg(sys.argv, log)
if options_storage.continue_mode:
cmd_line, options = get_options_from_params(os.path.join(options_storage.output_dir, "params.txt"))
if not options:
support.error("failed to parse command line of the previous run! Please restart from the beginning.")
cfg, dataset_data = fill_cfg(options, log)
options_storage.continue_mode = True
log_filename = os.path.join(cfg["common"].output_dir, "spades.log")
if options_storage.continue_mode:
log_handler = logging.FileHandler(log_filename, mode='a')
else:
log_handler = logging.FileHandler(log_filename, mode='w')
log.addHandler(log_handler)
if options_storage.continue_mode:
log.info("\n======= SPAdes pipeline continued. Log can be found here: " + log_filename + "\n")
log.info("Restored from " + cmd_line)
else:
params_filename = os.path.join(cfg["common"].output_dir, "params.txt")
params_handler = logging.FileHandler(params_filename, mode='w')
log.addHandler(params_handler)
command = "Command line:"
for v in sys.argv:
command += " " + v
log.info(command)
print_used_values(cfg, log)
log.removeHandler(params_handler)
log.info("\n======= SPAdes pipeline started. Log can be found here: " + log_filename + "\n")
# splitting interlaced reads if needed
if support.dataset_has_interlaced_reads(dataset_data):
dir_for_split_reads = os.path.join(os.path.abspath(options_storage.output_dir), 'split_reads')
if not os.path.isdir(dir_for_split_reads):
os.makedirs(dir_for_split_reads)
dataset_data = support.split_interlaced_reads(dataset_data, dir_for_split_reads, log)
options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
pyyaml.dump(dataset_data, open(options_storage.dataset_yaml_filename, 'w'))
cfg["dataset"].yaml_filename = os.path.abspath(options_storage.dataset_yaml_filename)
try:
# copying configs before all computations (to prevent its changing at run time)
tmp_configs_dir = os.path.join(cfg["common"].output_dir, "configs")
if os.path.isdir(tmp_configs_dir) and not options_storage.continue_mode:
shutil.rmtree(tmp_configs_dir)
if not os.path.isdir(tmp_configs_dir):
shutil.copytree(os.path.join(spades_home, "configs"), tmp_configs_dir)
corrected_dataset_yaml_filename = ''
if "error_correction" in cfg:
bh_cfg = merge_configs(cfg["error_correction"], cfg["common"])
bh_cfg.__dict__["dataset_yaml_filename"] = cfg["dataset"].yaml_filename
corrected_dataset_yaml_filename = os.path.join(bh_cfg.output_dir, "corrected.yaml")
if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode:
log.info("\n===== Skipping read error correction (already processed). \n")
else:
options_storage.continue_mode = False # continue from here
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in bh_cfg.__dict__:
os.environ["HEAPCHECK"] = bh_cfg.heap_check
if os.path.exists(bh_cfg.output_dir):
shutil.rmtree(bh_cfg.output_dir)
os.makedirs(bh_cfg.output_dir)
if not os.path.exists(bh_cfg.tmp_dir):
os.makedirs(bh_cfg.tmp_dir)
log.info("\n===== Read error correction started. \n")
bh_logic.run_bh(corrected_dataset_yaml_filename, tmp_configs_dir, bin_home, bh_cfg,
ext_python_modules_home, log)
log.info("\n===== Read error correction finished. \n")
result_contigs_filename = os.path.join(cfg["common"].output_dir, "contigs.fasta")
result_scaffolds_filename = os.path.join(cfg["common"].output_dir, "scaffolds.fasta")
misc_dir = os.path.join(cfg["common"].output_dir, "misc")
### if mismatch correction is enabled then result contigs are copied to misc directory
assembled_contigs_filename = os.path.join(misc_dir, "assembled_contigs.fasta")
assembled_scaffolds_filename = os.path.join(misc_dir, "assembled_scaffolds.fasta")
if "assembly" in cfg:
spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
spades_cfg.__dict__["result_contigs"] = result_contigs_filename
spades_cfg.__dict__["result_scaffolds"] = result_scaffolds_filename
spades_cfg.__dict__["additional_contigs"] = os.path.join(spades_cfg.output_dir, "simplified_contigs.fasta")
if options_storage.continue_mode and (os.path.isfile(spades_cfg.result_contigs)
or ("mismatch_corrector" in cfg and
os.path.isfile(assembled_contigs_filename))):
log.info("\n===== Skipping assembling (already processed). \n")
# calculating latest_dir for the next stages
latest_dir = support.get_latest_dir(os.path.join(spades_cfg.output_dir, "K*"))
if not latest_dir:
support.error("failed to continue the previous run! Please restart from the beginning.")
else:
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))
if support.dataset_has_paired_reads(dataset_data):
spades_cfg.__dict__["paired_mode"] = True
else:
spades_cfg.__dict__["paired_mode"] = False
if options_storage.rectangles:
spades_cfg.__dict__["resolving_mode"] = "rectangles"
if "HEAPCHECK" in os.environ:
del os.environ["HEAPCHECK"]
if "heap_check" in spades_cfg.__dict__:
os.environ["HEAPCHECK"] = spades_cfg.heap_check
log.info("\n===== Assembling started.\n")
# creating dataset
dataset_filename = os.path.join(spades_cfg.output_dir, "dataset.info")
if not os.path.isfile(dataset_filename) or not options_storage.continue_mode:
dataset_file = open(dataset_filename, 'w')
import process_cfg
dataset_file.write("single_cell" + '\t' + process_cfg.bool_to_str(cfg["dataset"].single_cell) + '\n')
if os.path.isfile(corrected_dataset_yaml_filename):
dataset_file.write("reads" + '\t' + process_cfg.process_spaces(corrected_dataset_yaml_filename) + '\n')
else:
dataset_file.write("reads" + '\t' + process_cfg.process_spaces(cfg["dataset"].yaml_filename) + '\n')
if spades_cfg.developer_mode and "reference" in cfg["dataset"].__dict__:
dataset_file.write("reference_genome" + '\t')
dataset_file.write(process_cfg.process_spaces(os.path.abspath(cfg["dataset"].reference)) + '\n')
dataset_file.close()
spades_cfg.__dict__["dataset"] = dataset_filename
latest_dir = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, log)
#rectangles
if spades_cfg.paired_mode and options_storage.rectangles:
if options_storage.continue_mode: # TODO: continue mode
support.warning("sorry, --continue doesn't work with --rectangles yet. Skipping repeat resolving.")
else:
sys.path.append(os.path.join(python_modules_home, "rectangles"))
import rrr
rrr_input_dir = os.path.join(latest_dir, "saves")
rrr_outpath = os.path.join(spades_cfg.output_dir, "rectangles")
if not os.path.exists(rrr_outpath):
os.mkdir(rrr_outpath)
rrr_reference_information_file = os.path.join(rrr_input_dir,
"late_pair_info_counted_etalon_distance.txt")
rrr_test_util = rrr.TestUtils(rrr_reference_information_file,
os.path.join(rrr_outpath, "rectangles.log"))
rrr.resolve(rrr_input_dir, rrr_outpath, rrr_test_util, "", cfg["dataset"].single_cell, spades_cfg.careful)
shutil.copyfile(os.path.join(rrr_outpath, "rectangles_extend_before_scaffold.fasta"), spades_cfg.result_contigs)
shutil.copyfile(os.path.join(rrr_outpath, "rectangles_extend.fasta"), spades_cfg.result_scaffolds)
if not spades_cfg.developer_mode:
if os.path.exists(rrr_input_dir):
shutil.rmtree(rrr_input_dir)
if os.path.exists(rrr_outpath):
shutil.rmtree(rrr_outpath, True)
if os.path.exists(rrr_outpath):
os.system('rm -r ' + rrr_outpath)
#EOR
if os.path.isdir(misc_dir) and not options_storage.continue_mode:
shutil.rmtree(misc_dir)
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
if os.path.isfile(spades_cfg.additional_contigs):
shutil.move(spades_cfg.additional_contigs, misc_dir)
log.info("\n===== Assembling finished. \n")
#corrector
if "mismatch_corrector" in cfg and (os.path.isfile(result_contigs_filename) or
(options_storage.continue_mode and os.path.isfile(assembled_contigs_filename))):
to_correct = dict()
to_correct["contigs"] = (result_contigs_filename, assembled_contigs_filename)
if os.path.isfile(result_scaffolds_filename) or (options_storage.continue_mode and
os.path.isfile(assembled_scaffolds_filename)):
to_correct["scaffolds"] = (result_scaffolds_filename, assembled_scaffolds_filename)
# moving assembled contigs (scaffolds) to misc dir
for k, (old, new) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(new):
continue
shutil.move(old, new)
if options_storage.continue_mode and os.path.isfile(result_contigs_filename) and \
(os.path.isfile(result_scaffolds_filename) or not os.path.isfile(assembled_scaffolds_filename)):
log.info("\n===== Skipping mismatch correction (already processed). \n")
else:
log.info("\n===== Mismatch correction started.")
# detecting paired-end library with the largest insert size
dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r')) ### initial dataset, i.e. before error correction
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(options_storage.dataset_yaml_filename))
paired_end_libraries_ids = []
for id, reads_library in enumerate(dataset_data):
if reads_library['type'] == 'paired-end':
paired_end_libraries_ids.append(id)
if not len(paired_end_libraries_ids):
support.error('Mismatch correction cannot be performed without at least one paired-end library!')
estimated_params = load_config_from_file(os.path.join(latest_dir, "_est_params.info"))
max_insert_size = -1
target_paired_end_library_id = -1
for id in paired_end_libraries_ids:
if float(estimated_params.__dict__["insert_size_" + str(id)]) > max_insert_size:
max_insert_size = float(estimated_params.__dict__["insert_size_" + str(id)])
target_paired_end_library_id = id
yaml_dirname = os.path.dirname(options_storage.dataset_yaml_filename)
cfg["mismatch_corrector"].__dict__["1"] = list(map(lambda x: os.path.join(yaml_dirname, x),
dataset_data[target_paired_end_library_id]['left reads']))
cfg["mismatch_corrector"].__dict__["2"] = list(map(lambda x: os.path.join(yaml_dirname, x),
dataset_data[target_paired_end_library_id]['right reads']))
cfg["mismatch_corrector"].__dict__["insert-size"] = round(max_insert_size)
#TODO: add reads orientation
import corrector
corrector_cfg = cfg["mismatch_corrector"]
args = []
for key, values in corrector_cfg.__dict__.items():
if key == "output-dir":
continue
# for processing list of reads
if not isinstance(values, list):
values = [values]
for value in values:
if len(key) == 1:
args.append('-' + key)
else:
args.append('--' + key)
if value:
args.append(value)
# processing contigs and scaffolds (or only contigs)
for k, (corrected, assembled) in to_correct.items():
if options_storage.continue_mode and os.path.isfile(corrected):
log.info("\n== Skipping processing of " + k + " (already processed)\n")
continue
options_storage.continue_mode = False
log.info("\n== Processing of " + k + "\n")
cur_args = args[:]
cur_args += ['-c', assembled]
tmp_dir_for_corrector = os.path.join(corrector_cfg.__dict__["output-dir"], "mismatch_corrector_" + k)
cur_args += ['--output-dir', tmp_dir_for_corrector]
# correcting
corrector.main(cur_args, ext_python_modules_home, log)
result_corrected_filename = os.path.abspath(os.path.join(tmp_dir_for_corrector, "corrected_contigs.fasta"))
# moving corrected contigs (scaffolds) to SPAdes output dir
if os.path.isfile(result_corrected_filename):
shutil.move(result_corrected_filename, corrected)
if os.path.isdir(tmp_dir_for_corrector):
shutil.rmtree(tmp_dir_for_corrector)
log.info("\n===== Mismatch correction finished.\n")
if not cfg["common"].developer_mode and os.path.isdir(tmp_configs_dir):
shutil.rmtree(tmp_configs_dir)
#log.info("")
if os.path.isdir(os.path.dirname(corrected_dataset_yaml_filename)):
log.info(" * Corrected reads are in " + os.path.dirname(corrected_dataset_yaml_filename) + "/")
if os.path.isfile(result_contigs_filename):
log.info(" * Assembled contigs are in " + result_contigs_filename)
if os.path.isfile(result_scaffolds_filename):
log.info(" * Assembled scaffolds are in " + result_scaffolds_filename)
#log.info("")
#breaking scaffolds
if os.path.isfile(result_scaffolds_filename):
if not os.path.isdir(misc_dir):
os.makedirs(misc_dir)
result_broken_scaffolds = os.path.join(misc_dir, "broken_scaffolds.fasta")
threshold = 3
if not os.path.isfile(result_broken_scaffolds) or not options_storage.continue_mode:
support.break_scaffolds(result_scaffolds_filename, threshold, result_broken_scaffolds)
#log.info(" * Scaffolds broken by " + str(threshold) + " Ns are in " + result_broken_scaffolds)
### printing WARNINGS SUMMARY
if not support.log_warnings(log):
log.info("\n======= SPAdes pipeline finished.") # otherwise it finished WITH WARNINGS
log.info("\nSPAdes log can be found here: " + log_filename)
log.info("")
log.info("Thank you for using SPAdes!")
log.removeHandler(log_handler)
except Exception:
_, exc, _ = sys.exc_info()
log.exception(exc)
support.error("exception caught", log)