def short_statistics(fasta_file):
lengths = list(fp.read_sequence_lengths(fasta_file).values())
if not lengths:
return 0, 0
total_size = sum(lengths)
return total_size, _calc_n50(lengths, total_size)
def setup_params(args):
logger.info("Configuring run")
parameters = {}
total_length = 0
read_lengths = []
for read_file in args.reads:
for seq, seq_len in fp.read_sequence_lengths(read_file).iteritems():
total_length += seq_len
read_lengths.append(seq_len)
_, reads_n50 = _calc_nx(read_lengths, total_length, 0.50)
_, reads_n90 = _calc_nx(read_lengths, total_length, 0.90)
#Selecting minimum overlap
logger.debug("Total sequence length: {0}".format(total_length))
coverage = total_length / args.genome_size
logger.info("Input genome size: {0}".format(args.genome_size))
logger.info("Estimated coverage: {0}".format(coverage))
if coverage < 5 or coverage > 1000:
logger.warning("Expected read coverage is " + str(coverage) +
", the assembly is not " +
"guaranteed to be optimal in this setting." +
" Are you sure that the genome size " +
"was entered correctly?")
logger.info("Reads N50/N90: {0} / {1}".format(reads_n50, reads_n90))
if args.min_overlap is None:
GRADE = 1000
int_min_ovlp = int(round(float(reads_n90) / GRADE)) * GRADE
parameters["min_overlap"] = \
max(cfg.vals["min_overlap_range"][args.read_type][0],
min(cfg.vals["min_overlap_range"][args.read_type][1], int_min_ovlp))
logger.info("Minimum overlap set to {0}".format(
parameters["min_overlap"]))
else:
parameters["min_overlap"] = args.min_overlap
#Selecting k-mer size
if args.genome_size < cfg.vals["big_genome_kmer"]:
parameters["kmer_size"] = cfg.vals["kmer_size"][args.read_type][0]
else:
parameters["kmer_size"] = cfg.vals["kmer_size"][args.read_type][1]
logger.info("Selected k-mer size: {0}".format(parameters["kmer_size"]))
#Downsampling reads for the first assembly stage to save memory
target_cov = None
if args.asm_coverage and args.asm_coverage < coverage:
target_cov = args.asm_coverage
#if not args.asm_coverage and args.genome_size >= 10 ** 9:
# target_cov = cfg.vals["reduced_asm_cov"]
if target_cov:
logger.info(
"Using longest {}x reads for contig assembly".format(target_cov))
min_read = _get_downsample_threshold(read_lengths,
args.genome_size * target_cov)
logger.debug("Min read length cutoff: {0}".format(min_read))
parameters["min_read_length"] = min_read
else:
parameters["min_read_length"] = 0
return parameters
def setup_params(args):
logger.info("Configuring run")
parameters = {}
parameters["pipeline_version"] = cfg.vals["pipeline_version"]
total_length = 0
read_lengths = []
MAX_READ_LEN = 2**31 - 1
lowest_read_len = cfg.vals["min_overlap_range"][args.read_type][0]
if args.min_overlap:
lowest_read_len = args.min_overlap
passing_reads = 0
for read_file in args.reads:
for _, seq_len in iteritems(fp.read_sequence_lengths(read_file)):
if seq_len > MAX_READ_LEN:
raise ConfigException(
"Length of single read in '{}' exceeded maximum ({})".
format(read_file, MAX_READ_LEN))
if seq_len > lowest_read_len:
passing_reads += 1
total_length += seq_len
read_lengths.append(seq_len)
if not passing_reads:
raise ConfigException(
"No reads above minimum length threshold ({})".format(
lowest_read_len))
_, reads_n50 = _calc_nx(read_lengths, total_length, 0.50)
_, reads_n90 = _calc_nx(read_lengths, total_length, 0.90)
#Selecting minimum overlap
logger.info("Total read length: %d", total_length)
if args.genome_size:
coverage = total_length // args.genome_size
logger.info("Input genome size: %d", args.genome_size)
logger.info("Estimated coverage: %d", coverage)
if coverage < 5 or coverage > 1000:
logger.warning("Expected read coverage is " + str(coverage) +
", the assembly is not " +
"guaranteed to be optimal in this setting." +
" Are you sure that the genome size " +
"was entered correctly?")
logger.info("Reads N50/N90: %d / %d", reads_n50, reads_n90)
if args.min_overlap is None:
GRADE = 1000
int_min_ovlp = int(round(reads_n90 / GRADE)) * GRADE
MIN_OVLP = cfg.vals["min_overlap_range"][args.read_type][0]
MAX_OVLP = cfg.vals["min_overlap_range"][args.read_type][1]
if args.meta:
MAX_OVLP = min(MAX_OVLP, cfg.vals["max_meta_overlap"])
parameters["min_overlap"] = max(MIN_OVLP, min(MAX_OVLP, int_min_ovlp))
logger.info("Minimum overlap set to %d", parameters["min_overlap"])
else:
parameters["min_overlap"] = args.min_overlap
logger.info("Selected minimum overlap: %d", parameters["min_overlap"])
#Selecting k-mer size
#parameters["kmer_size"] = cfg.vals["kmer_size"][args.read_type]
#logger.info("Selected k-mer size: %d", parameters["kmer_size"])
#Downsampling reads for the first assembly stage to save memory
target_cov = None
if args.asm_coverage and args.asm_coverage < coverage:
target_cov = args.asm_coverage
if target_cov:
logger.info("Using longest %dx reads for contig assembly", target_cov)
min_read = _get_downsample_threshold(read_lengths,
args.genome_size * target_cov)
logger.debug("Min read length cutoff: %d", min_read)
parameters["min_read_length"] = min_read
else:
parameters["min_read_length"] = 0
return parameters
def setup_params(args):
logger.info("Configuring run")
parameters = {}
parameters["pipeline_version"] = cfg.vals["pipeline_version"]
total_length = 0
read_lengths = []
for read_file in args.reads:
for _, seq_len in iteritems(fp.read_sequence_lengths(read_file)):
total_length += seq_len
read_lengths.append(seq_len)
_, reads_n50 = _calc_nx(read_lengths, total_length, 0.50)
_, reads_n90 = _calc_nx(read_lengths, total_length, 0.90)
#Selecting minimum overlap
logger.info("Total read length: %d", total_length)
coverage = total_length // args.genome_size
logger.info("Input genome size: %d", args.genome_size)
logger.info("Estimated coverage: %d", coverage)
if coverage < 5 or coverage > 1000:
logger.warning("Expected read coverage is " + str(coverage) +
", the assembly is not " +
"guaranteed to be optimal in this setting." +
" Are you sure that the genome size " +
"was entered correctly?")
logger.info("Reads N50/N90: %d / %d", reads_n50, reads_n90)
if args.min_overlap is None:
GRADE = 1000
int_min_ovlp = int(round(reads_n90 / GRADE)) * GRADE
MIN_OVLP = cfg.vals["min_overlap_range"][args.read_type][0]
MAX_OVLP = cfg.vals["min_overlap_range"][args.read_type][1]
if args.meta:
MAX_OVLP = min(MAX_OVLP, cfg.vals["max_meta_overlap"])
parameters["min_overlap"] = max(MIN_OVLP, min(MAX_OVLP, int_min_ovlp))
logger.info("Minimum overlap set to %d", parameters["min_overlap"])
else:
parameters["min_overlap"] = args.min_overlap
logger.info("Selected minimum overlap: %d", parameters["min_overlap"])
#Selecting k-mer size
if args.genome_size < cfg.vals["big_genome_kmer"]:
parameters["kmer_size"] = cfg.vals["kmer_size"][args.read_type][0]
else:
parameters["kmer_size"] = cfg.vals["kmer_size"][args.read_type][1]
logger.info("Selected k-mer size: %d", parameters["kmer_size"])
#Downsampling reads for the first assembly stage to save memory
target_cov = None
if args.asm_coverage and args.asm_coverage < coverage:
target_cov = args.asm_coverage
#if not args.asm_coverage and args.genome_size >= 10 ** 9:
# target_cov = cfg.vals["reduced_asm_cov"]
if target_cov:
logger.info("Using longest %dx reads for contig assembly", target_cov)
min_read = _get_downsample_threshold(read_lengths,
args.genome_size * target_cov)
logger.debug("Min read length cutoff: %d", min_read)
parameters["min_read_length"] = min_read
else:
parameters["min_read_length"] = 0
return parameters
