def generate_config(self, cfg):
data_dir = os.path.join(cfg.output_dir, "K%d" % self.K)
saves_dir = os.path.join(data_dir, "saves")
dst_configs = os.path.join(data_dir, "configs")
if self.get_stage(self.short_name) == options_storage.BASE_STAGE:
if not os.path.isdir(data_dir):
os.makedirs(data_dir)
dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False)
if self.prev_K:
additional_contigs_fname = os.path.join(cfg.output_dir, "K%d" % self.prev_K, "simplified_contigs.fasta")
else:
additional_contigs_fname = None
if "read_buffer_size" in cfg.__dict__:
# FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "construction.info"),
{"read_buffer_size": cfg.read_buffer_size}, self.log)
if "scaffolding_mode" in cfg.__dict__:
# FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "pe_params.info"),
{"scaffolding_mode": cfg.scaffolding_mode}, self.log)
prepare_config_rnaspades(os.path.join(dst_configs, "rna_mode.info"), self.log)
prepare_config_construction(os.path.join(dst_configs, "construction.info"), self.log)
cfg_fn = os.path.join(dst_configs, "config.info")
prepare_config_spades(cfg_fn, cfg, self.log, additional_contigs_fname, self.K, self.get_stage(self.short_name),
saves_dir, self.last_one, self.bin_home)
def PrepareConfigs(params, log):
CopyConfigs(params, log)
param_dict = CreateParamDict(params)
if not os.path.exists(params.config_file):
log.info("ERROR: config file was not found")
sys.exit(1)
process_cfg.substitute_params(params.config_file, param_dict, log)
def run_scaffold_correction(configs_dir, execution_home, cfg, log, latest, K):
data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K)
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
log.info("\n== Running scaffold correction \n")
scaffolds_file = os.path.join(latest, "scaffolds.fasta")
if not os.path.isfile(scaffolds_file):
support.error("Scaffodls were not found in " + scaffolds_file, log)
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs, "construction.info")
process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, log)
process_cfg.substitute_params(os.path.join(dst_configs, "moleculo_mode.info"), {"scaffolds_file": scaffolds_file}, log)
prepare_config_scaffold_correction(cfg_file_name, cfg, log, saves_dir, K)
command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
add_configs(command, dst_configs)
log.info(str(command))
support.sys_call(command, log)
def PrepareConfigs(params, log):
CopyConfigs(params, log)
param_dict = CreateParamDict(params)
if not os.path.exists(params.config_file):
log.info("ERROR: config file was not found")
sys.exit(1)
process_cfg.substitute_params(params.config_file, param_dict, log)
def run_scaffold_correction(configs_dir, execution_home, cfg, log, K):
data_dir = os.path.join(cfg.output_dir, "SCC")
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
# removing template configs
for root, dirs, files in os.walk(dst_configs):
for cfg_file in files:
cfg_file = os.path.join(root, cfg_file)
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
else:
os.rename(cfg_file, cfg_file.split('.template')[0])
log.info("\n== Running scaffold correction \n")
latest = os.path.join(cfg.output_dir, "K%d" % K)
scaffolds_file = os.path.join(latest, "scaffolds.fasta")
if not os.path.isfile(scaffolds_file):
support.error("Scaffodls were not found in " + scaffolds_file, log)
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs, "construction.info")
process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, log)
prepare_config_scaffold_correction(cfg_file_name, cfg, log, saves_dir, scaffolds_file)
command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
log.info(str(command))
support.sys_call(command, log)
def prepare_config_rnaspades(filename, log):
if not options_storage.rna:
return
subst_dict = dict()
subst_dict["ss_enabled"] = bool_to_str(options_storage.strand_specific is not None)
subst_dict["antisense"] = bool_to_str(options_storage.strand_specific)
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_spades(filename, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["run_mode"] = "false"
if "diploid_mode" in cfg.__dict__:
subst_dict["diploid_mode"] = bool_to_str(cfg.diploid_mode)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
if additional_contigs_fname:
subst_dict["additional_contigs"] = process_cfg.process_spaces(additional_contigs_fname)
subst_dict["use_additional_contigs"] = bool_to_str(True)
else:
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(last_one)
subst_dict["entry_point"] = stage
subst_dict["load_from"] = saves_dir
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one)
subst_dict["rr_enable"] = bool_to_str(last_one and cfg.rr_enable)
# subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["correct_mismatches"] = bool_to_str(last_one)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "careful" in cfg.__dict__:
subst_dict["mismatch_careful"] = bool_to_str(cfg.careful)
if "pacbio_mode" in cfg.__dict__:
subst_dict["pacbio_test_on"] = bool_to_str(cfg.pacbio_mode)
subst_dict["pacbio_reads"] = process_cfg.process_spaces(cfg.pacbio_reads)
process_cfg.substitute_params(filename, subst_dict, log)
def run_scaffold_correction(configs_dir, execution_home, cfg, log, K):
data_dir = os.path.join(cfg.output_dir, "SCC")
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
# removing template configs
for root, dirs, files in os.walk(dst_configs):
for cfg_file in files:
cfg_file = os.path.join(root, cfg_file)
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
else:
os.rename(cfg_file, cfg_file.split('.template')[0])
log.info("\n== Running scaffold correction \n")
latest = os.path.join(cfg.output_dir, "K%d" % K)
scaffolds_file = os.path.join(latest, "scaffolds.fasta")
if not os.path.isfile(scaffolds_file):
support.error("Scaffodls were not found in " + scaffolds_file, log)
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs, "construction.info")
process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, log)
prepare_config_scaffold_correction(cfg_file_name, cfg, log, saves_dir, scaffolds_file)
command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
log.info(str(command))
support.sys_call(command, log)
def prepare_config_spades(filename, cfg, log, use_additional_contigs, K,
last_one):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["run_mode"] = "false"
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["additional_contigs"] = process_cfg.process_spaces(
cfg.additional_contigs)
subst_dict["entry_point"] = "construction"
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one)
subst_dict["paired_mode"] = bool_to_str(last_one and cfg.paired_mode)
subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["use_additional_contigs"] = bool_to_str(use_additional_contigs)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["correct_mismatches"] = bool_to_str(last_one)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "careful" in cfg.__dict__:
subst_dict["mismatch_careful"] = bool_to_str(cfg.careful)
process_cfg.substitute_params(filename, subst_dict, log)
def generate_config(self, cfg):
K = cfg.iterative_K[-1]
latest = os.path.join(cfg.output_dir, "K%d" % K)
K = options_storage.SCC_K
data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K)
saves_dir = os.path.join(data_dir, "saves")
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if os.path.isdir(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"),
dst_configs,
preserve_times=False)
scaffolds_file = os.path.join(latest, "scaffolds.fasta")
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs,
"construction.info")
process_cfg.substitute_params(
construction_cfg_file_name,
{"read_buffer_size": cfg.read_buffer_size}, self.log)
process_cfg.substitute_params(
os.path.join(dst_configs, "moleculo_mode.info"),
{"scaffolds_file": scaffolds_file}, self.log)
prepare_config_scaffold_correction(cfg_file_name, cfg, self.log,
saves_dir, K)
def run_scaffold_correction(configs_dir, execution_home, cfg, log, latest, K):
data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K)
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"),
dst_configs,
preserve_times=False)
log.info("\n== Running scaffold correction \n")
scaffolds_file = os.path.join(latest, "scaffolds.fasta")
if not os.path.isfile(scaffolds_file):
support.error("Scaffodls were not found in " + scaffolds_file, log)
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs,
"construction.info")
process_cfg.substitute_params(
construction_cfg_file_name,
{"read_buffer_size": cfg.read_buffer_size}, log)
process_cfg.substitute_params(
os.path.join(dst_configs, "moleculo_mode.info"),
{"scaffolds_file": scaffolds_file}, log)
prepare_config_scaffold_correction(cfg_file_name, cfg, log, saves_dir, K)
command = [
os.path.join(execution_home, "spades-truseq-scfcorrection"),
cfg_file_name
]
add_configs(command, dst_configs)
log.info(str(command))
support.sys_call(command, log)
def run_iteration(configs_dir, execution_home, cfg, log, K, prev_K, last_one):
data_dir = os.path.join(cfg.output_dir, "K%d" % K)
stage = BASE_STAGE
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if options_storage.continue_mode:
if os.path.isfile(os.path.join(data_dir, "final_contigs.fasta")) and not (options_storage.restart_from and
(options_storage.restart_from == ("k%d" % K) or options_storage.restart_from.startswith("k%d:" % K))):
log.info("\n== Skipping assembler: " + ("K%d" % K) + " (already processed)")
return
if options_storage.restart_from and options_storage.restart_from.find(":") != -1:
stage = options_storage.restart_from[options_storage.restart_from.find(":") + 1:]
support.continue_from_here(log)
if stage != BASE_STAGE:
if not os.path.isdir(saves_dir):
support.error("Cannot restart from stage %s: saves were not found (%s)!" % (stage, saves_dir))
else:
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
shutil.copytree(os.path.join(configs_dir, "debruijn"), dst_configs)
# removing template configs
for root, dirs, files in os.walk(dst_configs):
for cfg_file in files:
cfg_file = os.path.join(root, cfg_file)
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
else:
os.rename(cfg_file, cfg_file.split('.template')[0])
log.info("\n== Running assembler: " + ("K%d" % K) + "\n")
if prev_K:
additional_contigs_fname = os.path.join(cfg.output_dir, "K%d" % prev_K, "simplified_contigs.fasta")
if not os.path.isfile(additional_contigs_fname):
support.warning("additional contigs for K=%d were not found (%s)!" % (K, additional_contigs_fname), log)
additional_contigs_fname = None
else:
additional_contigs_fname = None
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs, "construction.info")
process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, log)
prepare_config_spades(cfg_file_name, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one)
command = [os.path.join(execution_home, "spades"), cfg_file_name]
## this code makes sense for src/debruijn/simplification.cpp: corrected_and_save_reads() function which is not used now
# bin_reads_dir = os.path.join(cfg.output_dir, ".bin_reads")
# if os.path.isdir(bin_reads_dir):
# if glob.glob(os.path.join(bin_reads_dir, "*_cor*")):
# for cor_filename in glob.glob(os.path.join(bin_reads_dir, "*_cor*")):
# cor_index = cor_filename.rfind("_cor")
# new_bin_filename = cor_filename[:cor_index] + cor_filename[cor_index + 4:]
# shutil.move(cor_filename, new_bin_filename)
support.sys_call(command, log)
def prepare_config_bgcspades(filename, cfg, log):
if not "set_of_hmms" in cfg.__dict__:
return
subst_dict = dict()
subst_dict["set_of_hmms"] = cfg.set_of_hmms
if options_storage.args.bio:
subst_dict["component_size_part"] = 1
subst_dict["set_copynumber"] = bool_to_str(True)
subst_dict["start_only_from_tips"] = bool_to_str(True)
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_mulksg(filename, cfg, log, additional_contigs_fname, K,
stage, saves_dir, last_one, execution_home):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
if additional_contigs_fname:
subst_dict["additional_contigs"] = process_cfg.process_spaces(
additional_contigs_fname)
subst_dict["use_additional_contigs"] = bool_to_str(True)
else:
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(last_one)
subst_dict["entry_point"] = stage
subst_dict["load_from"] = saves_dir
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one or K >= 55)
subst_dict["rr_enable"] = bool_to_str(last_one and cfg.rr_enable)
# subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
#TODO: If on multi node, max_threads and max_memory need to change!!!
if K == cfg.iterative_K[-1]:
subst_dict["max_threads"] = min(multiprocessing.cpu_count(),
cfg.max_threads)
subst_dict["max_memory"] = cfg.max_memory
else:
subst_dict["max_threads"] = min(
multiprocessing.cpu_count(),
cfg.max_threads) #/(len(cfg.iterative_K)-1)
subst_dict["max_memory"] = cfg.max_memory / (len(cfg.iterative_K) - 1)
subst_dict["save_gp"] = bool_to_str(cfg.save_gp)
if (not last_one):
subst_dict["correct_mismatches"] = bool_to_str(False)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "pacbio_mode" in cfg.__dict__:
subst_dict["pacbio_test_on"] = bool_to_str(cfg.pacbio_mode)
subst_dict["pacbio_reads"] = process_cfg.process_spaces(
cfg.pacbio_reads)
if cfg.cov_cutoff == "off":
subst_dict["use_coverage_threshold"] = bool_to_str(False)
else:
subst_dict["use_coverage_threshold"] = bool_to_str(True)
if cfg.cov_cutoff == "auto":
subst_dict["coverage_threshold"] = 0.0
else:
subst_dict["coverage_threshold"] = cfg.cov_cutoff
if cfg.lcer_cutoff is not None:
subst_dict["lcer_enabled"] = bool_to_str(True)
subst_dict["lcer_coverage_threshold"] = cfg.lcer_cutoff
if "series_analysis" in cfg.__dict__:
subst_dict["series_analysis"] = cfg.series_analysis
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config(config_fname, ds_args, log):
args_dict = dict()
args_dict["tails_lie_on_bulges"] = process_cfg.bool_to_str(ds_args.allow_gaps)
args_dict["align_bulge_sides"] = process_cfg.bool_to_str(ds_args.weak_align)
args_dict["haplocontigs"] = process_cfg.process_spaces(ds_args.haplocontigs)
args_dict["output_dir"] = process_cfg.process_spaces(ds_args.output_dir)
args_dict["developer_mode"] = "false" #process_cfg.bool_to_str(False)
args_dict["tmp_dir"] = process_cfg.process_spaces(ds_args.tmp_dir)
args_dict["max_threads"] = ds_args.max_threads
args_dict["max_memory"] = ds_args.max_memory
process_cfg.substitute_params(config_fname, args_dict, log)
def create_mulksg_configs(configs_dir, execution_home, cfg, log, K_values_list,
additional_contigs_fname, last_one,
ext_python_modules_home):
command_list = []
contig_files = []
for K in K_values_list:
# RL = get_read_length(cfg.output_dir, K, ext_python_modules_home, log)
# if K >= RL:
# support.warning("Value of K (%d) exceeded estimated read length (%d)" %
# (K, RL), log)
data_dir = os.path.join(cfg.output_dir, "K%d" % K)
stage = BASE_STAGE
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util._path_created = {
} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"),
dst_configs,
preserve_times=False)
log.info("\n== Running assembler: " + ("K%d" % K) + "\n")
if "read_buffer_size" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(
os.path.join(dst_configs, "construction.info"),
{"read_buffer_size": cfg.read_buffer_size}, log)
if "scaffolding_mode" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(
os.path.join(dst_configs, "pe_params.info"),
{"scaffolding_mode": cfg.scaffolding_mode}, log)
prepare_config_rnamulksg(os.path.join(dst_configs, "rna_mode.info"),
log)
prepare_config_construction(
os.path.join(dst_configs, "construction.info"), log)
cfg_fn = os.path.join(dst_configs, "config.info")
prepare_config_mulksg(cfg_fn, cfg, log, additional_contigs_fname, K,
stage, saves_dir, last_one, execution_home)
command = [os.path.join(execution_home, "mulksg-core"), cfg_fn]
# print("command is: ", command)
add_configs(command, dst_configs)
command_list.append(command)
contig_files.append(
os.path.join(cfg.output_dir, "K%d" % K,
"simplified_contigs.fasta"))
return command_list, contig_files
def run_iteration(configs_dir, execution_home, cfg, log, K, prev_K, last_one):
data_dir = os.path.join(cfg.output_dir, "K%d" % K)
stage = BASE_STAGE
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
if options_storage.continue_mode:
if os.path.isfile(os.path.join(data_dir, "final_contigs.fasta")) and not (options_storage.restart_from and
(options_storage.restart_from == ("k%d" % K) or options_storage.restart_from.startswith("k%d:" % K))):
log.info("\n== Skipping assembler: " + ("K%d" % K) + " (already processed)")
return
if options_storage.restart_from and options_storage.restart_from.find(":") != -1 \
and options_storage.restart_from.startswith("k%d:" % K):
stage = options_storage.restart_from[options_storage.restart_from.find(":") + 1:]
support.continue_from_here(log)
if stage != BASE_STAGE:
if not os.path.isdir(saves_dir):
support.error("Cannot restart from stage %s: saves were not found (%s)!" % (stage, saves_dir))
else:
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
log.info("\n== Running assembler: " + ("K%d" % K) + "\n")
if prev_K:
additional_contigs_fname = os.path.join(cfg.output_dir, "K%d" % prev_K, "simplified_contigs.fasta")
if not os.path.isfile(additional_contigs_fname):
support.warning("additional contigs for K=%d were not found (%s)!" % (K, additional_contigs_fname), log)
additional_contigs_fname = None
else:
additional_contigs_fname = None
if "read_buffer_size" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "construction.info"), {"read_buffer_size": cfg.read_buffer_size}, log)
if "scaffolding_mode" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "pe_params.info"), {"scaffolding_mode": cfg.scaffolding_mode}, log)
prepare_config_rnaspades(os.path.join(dst_configs, "rna_mode.info"), log)
prepare_config_construction(os.path.join(dst_configs, "construction.info"), log)
cfg_fn = os.path.join(dst_configs, "config.info")
prepare_config_spades(cfg_fn, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one, execution_home)
command = [os.path.join(execution_home, "spades-core"), cfg_fn]
add_configs(command, dst_configs)
#print("Calling: " + " ".join(command))
support.sys_call(command, log)
def run_iteration(configs_dir, execution_home, cfg, log, K, prev_K, last_one):
data_dir = os.path.join(cfg.output_dir, "K%d" % K)
stage = BASE_STAGE
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
if options_storage.continue_mode:
if os.path.isfile(os.path.join(data_dir, "final_contigs.fasta")) and not (options_storage.restart_from and
(options_storage.restart_from == ("k%d" % K) or options_storage.restart_from.startswith("k%d:" % K))):
log.info("\n== Skipping assembler: " + ("K%d" % K) + " (already processed)")
return
if options_storage.restart_from and options_storage.restart_from.find(":") != -1 \
and options_storage.restart_from.startswith("k%d:" % K):
stage = options_storage.restart_from[options_storage.restart_from.find(":") + 1:]
support.continue_from_here(log)
if stage != BASE_STAGE:
if not os.path.isdir(saves_dir):
support.error("Cannot restart from stage %s: saves were not found (%s)!" % (stage, saves_dir))
else:
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
log.info("\n== Running assembler: " + ("K%d" % K) + "\n")
if prev_K:
additional_contigs_fname = os.path.join(cfg.output_dir, "K%d" % prev_K, "simplified_contigs.fasta")
if not os.path.isfile(additional_contigs_fname):
support.warning("additional contigs for K=%d were not found (%s)!" % (K, additional_contigs_fname), log)
additional_contigs_fname = None
else:
additional_contigs_fname = None
if "read_buffer_size" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "construction.info"), {"read_buffer_size": cfg.read_buffer_size}, log)
if "scaffolding_mode" in cfg.__dict__:
#FIXME why here???
process_cfg.substitute_params(os.path.join(dst_configs, "pe_params.info"), {"scaffolding_mode": cfg.scaffolding_mode}, log)
prepare_config_rnaspades(os.path.join(dst_configs, "rna_mode.info"), log)
prepare_config_construction(os.path.join(dst_configs, "construction.info"), log)
cfg_fn = os.path.join(dst_configs, "config.info")
prepare_config_spades(cfg_fn, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one, execution_home)
command = [os.path.join(execution_home, "spades-core"), cfg_fn]
add_configs(command, dst_configs)
#print("Calling: " + " ".join(command))
support.sys_call(command, log)
def prepare_config_spades(filename, cfg, log, additional_contigs_fname, K,
stage, saves_dir, last_one, execution_home):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
if additional_contigs_fname:
subst_dict["additional_contigs"] = process_cfg.process_spaces(
additional_contigs_fname)
subst_dict["use_additional_contigs"] = bool_to_str(True)
else:
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(last_one)
subst_dict["entry_point"] = stage
subst_dict["load_from"] = saves_dir
if "checkpoints" in cfg.__dict__:
subst_dict["checkpoints"] = cfg.checkpoints
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["time_tracer_enabled"] = bool_to_str(cfg.time_tracer)
subst_dict["gap_closer_enable"] = bool_to_str(
last_one or K >= options_storage.GAP_CLOSER_ENABLE_MIN_K)
subst_dict["rr_enable"] = bool_to_str(last_one and cfg.rr_enable)
# subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["save_gp"] = bool_to_str(cfg.save_gp)
if not last_one:
subst_dict["correct_mismatches"] = bool_to_str(False)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "pacbio_mode" in cfg.__dict__:
subst_dict["pacbio_test_on"] = bool_to_str(cfg.pacbio_mode)
subst_dict["pacbio_reads"] = process_cfg.process_spaces(
cfg.pacbio_reads)
if cfg.cov_cutoff == "off":
subst_dict["use_coverage_threshold"] = bool_to_str(False)
else:
subst_dict["use_coverage_threshold"] = bool_to_str(True)
if cfg.cov_cutoff == "auto":
subst_dict["coverage_threshold"] = 0.0
else:
subst_dict["coverage_threshold"] = cfg.cov_cutoff
if cfg.lcer_cutoff is not None:
subst_dict["lcer_enabled"] = bool_to_str(True)
subst_dict["lcer_coverage_threshold"] = cfg.lcer_cutoff
if "series_analysis" in cfg.__dict__:
subst_dict["series_analysis"] = cfg.series_analysis
process_cfg.substitute_params(filename, subst_dict, log)
def run_iteration(configs_dir, execution_home, cfg, log, K, prev_K, last_one):
data_dir = os.path.join(cfg.output_dir, "K%d" % K)
stage = BASE_STAGE
saves_dir = os.path.join(data_dir, 'saves')
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
if options_storage.continue_mode:
if os.path.isfile(os.path.join(data_dir, "final_contigs.fasta")) and not (options_storage.restart_from and
(options_storage.restart_from == ("k%d" % K) or options_storage.restart_from.startswith("k%d:" % K))):
log.info("\n== Skipping assembler: " + ("K%d" % K) + " (already processed)")
return
if options_storage.restart_from and options_storage.restart_from.find(":") != -1:
stage = options_storage.restart_from[options_storage.restart_from.find(":") + 1:]
support.continue_from_here(log)
if stage != BASE_STAGE:
if not os.path.isdir(saves_dir):
support.error("Cannot restart from stage %s: saves were not found (%s)!" % (stage, saves_dir))
else:
if os.path.exists(data_dir):
shutil.rmtree(data_dir)
os.makedirs(data_dir)
dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
# removing template configs
for root, dirs, files in os.walk(dst_configs):
for cfg_file in files:
cfg_file = os.path.join(root, cfg_file)
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
else:
os.rename(cfg_file, cfg_file.split('.template')[0])
log.info("\n== Running assembler: " + ("K%d" % K) + "\n")
if prev_K:
additional_contigs_fname = os.path.join(cfg.output_dir, "K%d" % prev_K, "simplified_contigs.fasta")
if not os.path.isfile(additional_contigs_fname):
support.warning("additional contigs for K=%d were not found (%s)!" % (K, additional_contigs_fname), log)
additional_contigs_fname = None
else:
additional_contigs_fname = None
if "read_buffer_size" in cfg.__dict__:
construction_cfg_file_name = os.path.join(dst_configs, "construction.info")
process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, log)
prepare_config_spades(cfg_file_name, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one, execution_home)
command = [os.path.join(execution_home, "spades"), cfg_file_name]
support.sys_call(command, log)
def prepare_config_spades(filename, cfg, log, additional_contigs_fname, K, stage, saves_dir, last_one, execution_home):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
if additional_contigs_fname:
subst_dict["additional_contigs"] = process_cfg.process_spaces(additional_contigs_fname)
subst_dict["use_additional_contigs"] = bool_to_str(True)
else:
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(last_one)
subst_dict["entry_point"] = stage
subst_dict["load_from"] = saves_dir
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one or K >= 55)
subst_dict["rr_enable"] = bool_to_str(last_one and cfg.rr_enable)
# subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["save_gp"] = bool_to_str(cfg.save_gp)
if (not last_one):
subst_dict["correct_mismatches"] = bool_to_str(False)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "pacbio_mode" in cfg.__dict__:
subst_dict["pacbio_test_on"] = bool_to_str(cfg.pacbio_mode)
subst_dict["pacbio_reads"] = process_cfg.process_spaces(cfg.pacbio_reads)
if cfg.cov_cutoff == "off":
subst_dict["use_coverage_threshold"] = bool_to_str(False)
else:
subst_dict["use_coverage_threshold"] = bool_to_str(True)
if cfg.cov_cutoff == "auto":
subst_dict["coverage_threshold"] = 0.0
else:
subst_dict["coverage_threshold"] = cfg.cov_cutoff
if cfg.lcer_cutoff is not None:
subst_dict["lcer_enabled"] = bool_to_str(True)
subst_dict["lcer_coverage_threshold"] = cfg.lcer_cutoff
#TODO: make something about spades.py and config param substitution
if "bwa_paired" in cfg.__dict__:
subst_dict["bwa_enable"] = bool_to_str(True)
subst_dict["path_to_bwa"] = os.path.join(execution_home, "bwa-spades")
if "series_analysis" in cfg.__dict__:
subst_dict["series_analysis"] = cfg.series_analysis
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config(config_fname, ds_args, log):
args_dict = dict()
args_dict["tails_lie_on_bulges"] = process_cfg.bool_to_str(not ds_args.allow_gaps)
args_dict["align_bulge_sides"] = process_cfg.bool_to_str(not ds_args.weak_align)
args_dict["haplocontigs"] = process_cfg.process_spaces(ds_args.haplocontigs)
args_dict["output_dir"] = process_cfg.process_spaces(ds_args.output_dir)
args_dict["developer_mode"] = process_cfg.bool_to_str(ds_args.dev_mode)
args_dict["tmp_dir"] = process_cfg.process_spaces(ds_args.tmp_dir)
args_dict["max_threads"] = ds_args.max_threads
args_dict["max_memory"] = ds_args.max_memory
args_dict["output_base"] = ""
args_dict["ha_enabled"] = process_cfg.bool_to_str(ds_args.haplotype_assembly)
args_dict["K"] = str(ds_args.k)
args_dict['saves'] = ds_args.saves
args_dict['entry_point'] = ds_args.start_from
process_cfg.substitute_params(config_fname, args_dict, log)
def prepare_config_bh(filename, cfg, log):
subst_dict = dict()
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset_yaml_filename)
subst_dict["input_working_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
subst_dict["output_dir"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["general_max_iterations"] = cfg.max_iterations
subst_dict["general_max_nthreads"] = cfg.max_threads
subst_dict["count_merge_nthreads"] = cfg.max_threads
subst_dict["bayes_nthreads"] = cfg.max_threads
subst_dict["expand_nthreads"] = cfg.max_threads
subst_dict["correct_nthreads"] = cfg.max_threads
subst_dict["general_hard_memory_limit"] = cfg.max_memory
if "qvoffset" in cfg.__dict__:
subst_dict["input_qvoffset"] = cfg.qvoffset
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config(config_fname, ds_args, log):
args_dict = dict()
args_dict["tails_lie_on_bulges"] = process_cfg.bool_to_str(not ds_args.allow_gaps)
args_dict["align_bulge_sides"] = process_cfg.bool_to_str(not ds_args.weak_align)
args_dict["haplocontigs"] = process_cfg.process_spaces(ds_args.haplocontigs)
args_dict["output_dir"] = process_cfg.process_spaces(ds_args.output_dir)
args_dict["developer_mode"] = process_cfg.bool_to_str(ds_args.dev_mode)
args_dict["tmp_dir"] = process_cfg.process_spaces(ds_args.tmp_dir)
args_dict["max_threads"] = ds_args.max_threads
args_dict["max_memory"] = ds_args.max_memory
args_dict["output_base"] = ""
args_dict["ha_enabled"] = process_cfg.bool_to_str(ds_args.haplotype_assembly)
args_dict["K"] = str(ds_args.k)
args_dict['saves'] = ds_args.saves
args_dict['entry_point'] = ds_args.start_from
process_cfg.substitute_params(config_fname, args_dict, log)
def prepare_config_scaffold_correction(filename, cfg, log, saves_dir, K):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(os.path.join(cfg.output_dir, "SCC"))
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(False)
subst_dict["entry_point"] = BASE_STAGE
subst_dict["load_from"] = saves_dir
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
#todo
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_bh(filename, cfg, log):
subst_dict = dict()
subst_dict["dataset"] = process_cfg.process_spaces(
cfg.dataset_yaml_filename)
subst_dict["input_working_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
subst_dict["output_dir"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["general_max_iterations"] = cfg.max_iterations
subst_dict["general_max_nthreads"] = cfg.max_threads
subst_dict["count_merge_nthreads"] = cfg.max_threads
subst_dict["bayes_nthreads"] = cfg.max_threads
subst_dict["expand_nthreads"] = cfg.max_threads
subst_dict["correct_nthreads"] = cfg.max_threads
subst_dict["general_hard_memory_limit"] = cfg.max_memory
if "qvoffset" in cfg.__dict__:
subst_dict["input_qvoffset"] = cfg.qvoffset
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_spades(filename, cfg, log, additional_contigs_fname, K,
stage, saves_dir, last_one):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["run_mode"] = "false"
if "diploid_mode" in cfg.__dict__:
subst_dict["diploid_mode"] = bool_to_str(cfg.diploid_mode)
subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset)
subst_dict["output_base"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir)
if additional_contigs_fname:
subst_dict["additional_contigs"] = process_cfg.process_spaces(
additional_contigs_fname)
subst_dict["use_additional_contigs"] = bool_to_str(True)
else:
subst_dict["use_additional_contigs"] = bool_to_str(False)
subst_dict["main_iteration"] = bool_to_str(last_one)
subst_dict["entry_point"] = stage
subst_dict["load_from"] = saves_dir
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one or K >= 55)
subst_dict["rr_enable"] = bool_to_str(last_one and cfg.rr_enable)
# subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["correct_mismatches"] = bool_to_str(last_one)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "careful" in cfg.__dict__:
subst_dict["mismatch_careful"] = bool_to_str(cfg.careful)
if "pacbio_mode" in cfg.__dict__:
subst_dict["pacbio_test_on"] = bool_to_str(cfg.pacbio_mode)
subst_dict["pacbio_reads"] = process_cfg.process_spaces(
cfg.pacbio_reads)
if cfg.cov_cutoff == "off":
subst_dict["use_coverage_threshold"] = bool_to_str(False)
else:
subst_dict["use_coverage_threshold"] = bool_to_str(True)
if cfg.cov_cutoff == "auto":
subst_dict["coverage_threshold"] = 0.0
else:
subst_dict["coverage_threshold"] = cfg.cov_cutoff
process_cfg.substitute_params(filename, subst_dict, log)
def ModifyConfigFiles(params, log):
cdr_param_dict = dict()
cdr_param_dict['input_reads'] = params.input_reads
cdr_param_dict['output_dir'] = params.output_dir
cdr_param_dict['vj_finder_config'] = params.vj_finder_config_file
cdr_param_dict['num_threads'] = params.num_threads
cdr_param_dict['domain_system'] = params.domain_system
cdr_param_dict['run_hg_constructor'] = os.path.join(home_directory, './build/release/bin/ig_swgraph_construct')
vj_param_dict = dict()
vj_param_dict['loci'] = params.loci
vj_param_dict['germline_dir'] = os.path.join(home_directory, "data/germline")
params.germline_config_file = os.path.join(params.vj_finder_config_dir, "germline_files_config.txt")
vj_param_dict['germline_filenames_config'] = params.germline_config_file
ModifyParamsWrtOrganism(params, cdr_param_dict, vj_param_dict)
process_cfg.substitute_params(params.cdr_labeler_config_file, cdr_param_dict, log)
process_cfg.substitute_params(params.vj_finder_config_file, vj_param_dict, log)
def ModifyConfigFiles(params, log):
cdr_param_dict = dict()
cdr_param_dict['input_reads'] = params.input_reads
cdr_param_dict['output_dir'] = params.output_dir
cdr_param_dict['vj_finder_config'] = params.vj_finder_config_file
cdr_param_dict['num_threads'] = params.num_threads
cdr_param_dict['domain_system'] = params.domain_system
cdr_param_dict['run_hg_constructor'] = os.path.join(home_directory, './build/release/bin/ig_swgraph_construct')
vj_param_dict = dict()
vj_param_dict['loci'] = params.loci
vj_param_dict['germline_dir'] = os.path.join(home_directory, "data/germline")
params.germline_config_file = os.path.join(params.vj_finder_config_dir, "germline_files_config.txt")
vj_param_dict['germline_filenames_config'] = params.germline_config_file
ModifyParamsWrtOrganism(params, cdr_param_dict, vj_param_dict)
process_cfg.substitute_params(params.cdr_labeler_config_file, cdr_param_dict, log)
process_cfg.substitute_params(params.vj_finder_config_file, vj_param_dict, log)
def prepare_config_bh(self, filename, cfg, log):
subst_dict = dict()
subst_dict["dataset"] = process_cfg.process_spaces(
cfg.dataset_yaml_filename)
subst_dict["input_working_dir"] = process_cfg.process_spaces(
cfg.tmp_dir)
subst_dict["output_dir"] = process_cfg.process_spaces(cfg.output_dir)
subst_dict["general_max_iterations"] = options_storage.ITERATIONS
subst_dict["general_max_nthreads"] = cfg.max_threads
subst_dict["count_merge_nthreads"] = cfg.max_threads
subst_dict["bayes_nthreads"] = cfg.max_threads
subst_dict["expand_nthreads"] = cfg.max_threads
subst_dict["correct_nthreads"] = cfg.max_threads
subst_dict["general_hard_memory_limit"] = cfg.max_memory
if "qvoffset" in cfg.__dict__:
subst_dict["input_qvoffset"] = cfg.qvoffset
if "count_filter_singletons" in cfg.__dict__:
subst_dict["count_filter_singletons"] = cfg.count_filter_singletons
if "read_buffer_size" in cfg.__dict__:
subst_dict["count_split_buffer"] = cfg.read_buffer_size
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_spades(filename, cfg, log, prev_K, K, last_one):
subst_dict = dict()
subst_dict["K"] = str(K)
subst_dict["run_mode"] = "false"
subst_dict["dataset"] = cfg.dataset
subst_dict["output_base"] = cfg.output_dir
subst_dict["additional_contigs"] = cfg.additional_contigs
subst_dict["entry_point"] = "construction"
subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode)
subst_dict["gap_closer_enable"] = bool_to_str(last_one)
subst_dict["paired_mode"] = bool_to_str(last_one and cfg.paired_mode)
subst_dict["topology_simplif_enabled"] = bool_to_str(last_one)
subst_dict["use_additional_contigs"] = bool_to_str(prev_K)
subst_dict["max_threads"] = cfg.max_threads
subst_dict["max_memory"] = cfg.max_memory
subst_dict["correct_mismatches"] = bool_to_str(last_one)
if "resolving_mode" in cfg.__dict__:
subst_dict["resolving_mode"] = cfg.resolving_mode
if "careful" in cfg.__dict__:
subst_dict["mismatch_careful"] = bool_to_str(cfg.careful)
process_cfg.substitute_params(filename, subst_dict, log)
def ModifyConfigFiles(params, log):
igs_params_dict = dict()
igs_params_dict['output_dir'] = params.output_dir
igs_params_dict['loci'] = params.loci
igs_params_dict['number_of_metaroots'] = params.number_of_metaroots
igs_params_dict['pool_manager_strategy'] = params.tree_strategy
igs_params_dict['germline_dir'] = os.path.join(home_directory, "data/germline")
igs_params_dict['cdr_labeler_config_filename'] = params.cdr_labeler_config_filename
cdr_params_dict = dict()
cdr_params_dict['vj_finder_config'] = params.vj_finder_config_filename
vjf_params_dict = dict()
params.germline_config_file = os.path.join(params.vj_finder_config_dir, "germline_files_config.txt")
vjf_params_dict['germline_filenames_config'] = params.germline_config_file
vjf_params_dict['germline_dir'] = os.path.join(home_directory, "data/germline")
igs_params_dict['germline_filenames_config'] = params.germline_config_file
cdr_params_dict = ModifyParamsWrtOrganism(params, cdr_params_dict)
process_cfg.substitute_params(params.output_config_file, igs_params_dict, log)
process_cfg.substitute_params(params.cdr_labeler_config_filename, cdr_params_dict, log)
process_cfg.substitute_params(params.vj_finder_config_filename, vjf_params_dict, log)
def prepare_config_construction(filename, log):
if options_storage.read_cov_threshold is None:
return
subst_dict = dict()
subst_dict["read_cov_threshold"] = options_storage.read_cov_threshold
process_cfg.substitute_params(filename, subst_dict, log)
def prepare_config_construction(filename, log):
if options_storage.read_cov_threshold is None:
return
subst_dict = dict()
subst_dict["read_cov_threshold"] = options_storage.read_cov_threshold
process_cfg.substitute_params(filename, subst_dict, log)
