def print_used_values(cfg, log):
def print_value(cfg, section, param, pretty_param="", margin=" "):
if not pretty_param:
pretty_param = param.capitalize().replace('_', ' ')
line = margin + pretty_param
if param in cfg[section].__dict__:
line += ": " + str(cfg[section].__dict__[param])
else:
if "offset" in param:
line += " will be auto-detected"
log.info(line)
log.info("")
# system info
log.info("System information:")
try:
log.info(" SPAdes version: " + str(spades_version).strip())
log.info(" Python version: " + ".".join(map(str, sys.version_info[0:3])))
# for more details: '[' + str(sys.version_info) + ']'
log.info(" OS: " + platform.platform())
# for more details: '[' + str(platform.uname()) + ']'
except Exception:
log.info(" Problem occurred when getting system information")
log.info("")
# main
print_value(cfg, "common", "output_dir", "", "")
if ("error_correction" in cfg) and (not "assembly" in cfg):
log.info("Mode: ONLY read error correction (without assembling)")
elif (not "error_correction" in cfg) and ("assembly" in cfg):
log.info("Mode: ONLY assembling (without read error correction)")
else:
log.info("Mode: read error correction and assembling")
if ("common" in cfg) and ("developer_mode" in cfg["common"].__dict__):
if cfg["common"].developer_mode:
log.info("Debug mode is turned ON")
else:
log.info("Debug mode is turned OFF")
log.info("")
# dataset
if "dataset" in cfg:
log.info("Dataset parameters:")
if options_storage.args.iontorrent:
log.info(" IonTorrent data")
if options_storage.args.bio:
log.info(" BiosyntheticSPAdes mode")
if options_storage.args.meta:
log.info(" Metagenomic mode")
elif options_storage.args.large_genome:
log.info(" Large genome mode")
elif options_storage.args.truseq_mode:
log.info(" Illumina TruSeq mode")
elif options_storage.args.isolate:
log.info(" Isolate mode")
elif options_storage.args.rna:
log.info(" RNA-seq mode")
elif options_storage.args.single_cell:
log.info(" Single-cell mode")
else:
log.info(" Standard mode")
log.info(" For multi-cell/isolate data we recommend to use '--isolate' option;" \
" for single-cell MDA data use '--sc';" \
" for metagenomic data use '--meta';" \
" for RNA-Seq use '--rna'.")
log.info(" Reads:")
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename))
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)
# error correction
if "error_correction" in cfg:
log.info("Read error correction parameters:")
print_value(cfg, "error_correction", "max_iterations", "Iterations")
print_value(cfg, "error_correction", "qvoffset", "PHRED offset")
if cfg["error_correction"].gzip_output:
log.info(" Corrected reads will be compressed")
else:
log.info(" Corrected reads will NOT be compressed")
# assembly
if "assembly" in cfg:
log.info("Assembly parameters:")
if options_storage.auto_K_allowed():
log.info(" k: automatic selection based on read length")
else:
print_value(cfg, "assembly", "iterative_K", "k")
if options_storage.args.plasmid:
log.info(" Plasmid mode is turned ON")
if cfg["assembly"].disable_rr:
log.info(" Repeat resolution is DISABLED")
else:
log.info(" Repeat resolution is enabled")
if options_storage.args.careful:
log.info(" Mismatch careful mode is turned ON")
else:
log.info(" Mismatch careful mode is turned OFF")
if "mismatch_corrector" in cfg:
log.info(" MismatchCorrector will be used")
else:
log.info(" MismatchCorrector will be SKIPPED")
if cfg["assembly"].cov_cutoff == "off":
log.info(" Coverage cutoff is turned OFF")
elif cfg["assembly"].cov_cutoff == "auto":
log.info(" Coverage cutoff is turned ON and threshold will be auto-detected")
else:
log.info(" Coverage cutoff is turned ON and threshold is %f" % cfg["assembly"].cov_cutoff)
log.info("Other parameters:")
print_value(cfg, "common", "tmp_dir", "Dir for temp files")
print_value(cfg, "common", "max_threads", "Threads")
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
def print_used_values(cfg, log):
def print_value(cfg, section, param, pretty_param="", margin=" "):
if not pretty_param:
pretty_param = param.capitalize().replace('_', ' ')
line = margin + pretty_param
if param in cfg[section].__dict__:
line += ": " + str(cfg[section].__dict__[param])
else:
if param.find("offset") != -1:
line += " will be auto-detected"
log.info(line)
log.info("")
# system info
log.info("System information:")
try:
log.info(" SPAdes version: " + str(spades_version).strip())
log.info(" Python version: " +
".".join(map(str, sys.version_info[0:3])))
# for more details: '[' + str(sys.version_info) + ']'
log.info(" OS: " + platform.platform())
# for more deatils: '[' + str(platform.uname()) + ']'
except Exception:
log.info(" Problem occurred when getting system information")
log.info("")
# main
print_value(cfg, "common", "output_dir", "", "")
if ("error_correction" in cfg) and (not "assembly" in cfg):
log.info("Mode: ONLY read error correction (without assembling)")
elif (not "error_correction" in cfg) and ("assembly" in cfg):
log.info("Mode: ONLY assembling (without read error correction)")
else:
log.info("Mode: read error correction and assembling")
if ("common" in cfg) and ("developer_mode" in cfg["common"].__dict__):
if cfg["common"].developer_mode:
log.info("Debug mode turned ON")
else:
log.info("Debug mode turned OFF")
log.info("")
# dataset
if "dataset" in cfg:
log.info("Dataset parameters:")
if cfg["dataset"].single_cell:
log.info(" Single-cell mode")
else:
log.info(" Multi-cell mode (you should set '--sc' flag if input data"\
" was obtained with MDA (single-cell) technology")
log.info(" Reads:")
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(
dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)
# error correction
if "error_correction" in cfg:
log.info("Read error correction parameters:")
print_value(cfg, "error_correction", "tmp_dir", "Dir for temp files")
print_value(cfg, "error_correction", "max_iterations", "Iterations")
print_value(cfg, "error_correction", "qvoffset", "PHRED offset")
if cfg["error_correction"].gzip_output:
log.info(" Corrected reads will be compressed (with gzip)")
else:
log.info(" Corrected reads will NOT be compressed (with gzip)")
# assembly
if "assembly" in cfg:
log.info("Assembly parameters:")
print_value(cfg, "assembly", "iterative_K", "k")
log.info("Other parameters:")
print_value(cfg, "common", "max_threads", "Threads")
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
def print_used_values(cfg, log):
def print_value(cfg, section, param, pretty_param="", margin=" "):
if not pretty_param:
pretty_param = param.capitalize().replace('_', ' ')
line = margin + pretty_param
if param in cfg[section].__dict__:
line += ": " + str(cfg[section].__dict__[param])
else:
if param.find("offset") != -1:
line += " will be auto-detected"
log.info(line)
log.info("")
# system info
log.info("System information:")
try:
log.info(" SPAdes version: " + str(spades_version).strip())
log.info(" Python version: " + ".".join(map(str, sys.version_info[0:3])))
# for more details: '[' + str(sys.version_info) + ']'
log.info(" OS: " + platform.platform())
# for more deatils: '[' + str(platform.uname()) + ']'
except Exception:
log.info(" Problem occurred when getting system information")
log.info("")
# main
print_value(cfg, "common", "output_dir", "", "")
if ("error_correction" in cfg) and (not "assembly" in cfg):
log.info("Mode: ONLY read error correction (without assembling)")
elif (not "error_correction" in cfg) and ("assembly" in cfg):
log.info("Mode: ONLY assembling (without read error correction)")
else:
log.info("Mode: read error correction and assembling")
if ("common" in cfg) and ("developer_mode" in cfg["common"].__dict__):
if cfg["common"].developer_mode:
log.info("Debug mode is turned ON")
else:
log.info("Debug mode is turned OFF")
log.info("")
# dataset
if "dataset" in cfg:
log.info("Dataset parameters:")
if cfg["dataset"].single_cell:
log.info(" Single-cell mode")
else:
log.info(" Multi-cell mode (you should set '--sc' flag if input data"\
" was obtained with MDA (single-cell) technology")
if cfg["dataset"].iontorrent:
log.info(" IonTorrent data")
log.info(" Reads:")
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)
# error correction
if "error_correction" in cfg:
log.info("Read error correction parameters:")
print_value(cfg, "error_correction", "max_iterations", "Iterations")
print_value(cfg, "error_correction", "qvoffset", "PHRED offset")
if cfg["error_correction"].gzip_output:
log.info(" Corrected reads will be compressed (with gzip)")
else:
log.info(" Corrected reads will NOT be compressed (with gzip)")
# assembly
if "assembly" in cfg:
log.info("Assembly parameters:")
if options_storage.auto_K_allowed():
log.info(" k: automatic selection based on read length")
else:
print_value(cfg, "assembly", "iterative_K", "k")
if cfg["assembly"].careful:
log.info(" Mismatch careful mode is turned ON")
else:
log.info(" Mismatch careful mode is turned OFF")
if cfg["assembly"].disable_rr:
log.info(" Repeat resolution is DISABLED")
else:
log.info(" Repeat resolution is enabled")
if "mismatch_corrector" in cfg:
log.info(" MismatchCorrector will be used")
else:
log.info(" MismatchCorrector will be SKIPPED")
log.info("Other parameters:")
print_value(cfg, "common", "tmp_dir", "Dir for temp files")
print_value(cfg, "common", "max_threads", "Threads")
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
def print_used_values(cfg, log):
def print_value(cfg, section, param, pretty_param="", margin=" "):
if not pretty_param:
pretty_param = param.capitalize().replace("_", " ")
line = margin + pretty_param
if param in cfg[section].__dict__:
line += ": " + str(cfg[section].__dict__[param])
else:
if param.find("offset") != -1:
line += " will be auto-detected"
log.info(line)
log.info("")
# system info
log.info("System information:")
try:
log.info(" SPAdes version: " + str(spades_version))
log.info(
" Python version: "
+ str(sys.version_info[0])
+ "."
+ str(sys.version_info[1])
+ "."
+ str(sys.version_info[2])
)
# for more details: '[' + str(sys.version_info) + ']'
log.info(" OS: " + platform.platform())
# for more deatils: '[' + str(platform.uname()) + ']'
except:
log.info(" Problem occurred when getting system information")
log.info("")
# main
print_value(cfg, "common", "output_dir", "", "")
if ("error_correction" in cfg) and (not "assembly" in cfg):
log.info("Mode: ONLY read error correction (without assembling)")
elif (not "error_correction" in cfg) and ("assembly" in cfg):
log.info("Mode: ONLY assembling (without read error correction)")
else:
log.info("Mode: read error correction and assembling")
if ("common" in cfg) and ("developer_mode" in cfg["common"].__dict__):
if cfg["common"].developer_mode:
log.info("Debug mode turned ON")
else:
log.info("Debug mode turned OFF")
log.info("")
# dataset
if "dataset" in cfg:
log.info("Dataset parameters:")
if cfg["dataset"].single_cell:
log.info(" Single-cell mode")
else:
log.info(
" Multi-cell mode (you should set '--sc' flag if input data"
" was obtained with MDA (single-cell) technology"
)
# TODO: nice output of reads
log.info(" Reads:")
support.pretty_print_reads(pyyaml.load(file(cfg["dataset"].yaml_filename, "r")), log)
# error correction
if "error_correction" in cfg:
log.info("Read error correction parameters:")
print_value(cfg, "error_correction", "tmp_dir", "Dir for temp files")
print_value(cfg, "error_correction", "max_iterations", "Iterations")
print_value(cfg, "error_correction", "qvoffset", "PHRED offset")
if cfg["error_correction"].gzip_output:
log.info(" Corrected reads will be compressed (with gzip)")
else:
log.info(" Corrected reads will NOT be compressed (with gzip)")
# assembly
if "assembly" in cfg:
log.info("Assembly parameters:")
print_value(cfg, "assembly", "iterative_K", "k")
log.info("Other parameters:")
print_value(cfg, "common", "max_threads", "Threads")
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")