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")
corrected_dataset_yaml_filename = bh_logic.run_bh(
tmp_configs_dir, bin_home, bh_cfg, ext_python_modules_home, log
)
log.info("\n===== Read error correction finished. \n")
result_contigs_filename = ""
result_scaffolds_filename = ""
misc_dir = os.path.join(cfg["common"].output_dir, "misc")
if "assembly" in cfg:
spades_cfg = merge_configs(cfg["assembly"], cfg["common"])
spades_cfg.__dict__["result_contigs"] = os.path.join(spades_cfg.output_dir, "contigs.fasta")
spades_cfg.__dict__["result_scaffolds"] = os.path.join(spades_cfg.output_dir, "scaffolds.fasta")
spades_cfg.__dict__["additional_contigs"] = os.path.join(spades_cfg.output_dir, "simplified_contigs.fasta")
if corrected_dataset_yaml_filename:
dataset_data = pyyaml.load(file(corrected_dataset_yaml_filename, "r"))
if support.dataset_has_paired_reads(dataset_data):
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():
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)
