def n50(args):
"""
%prog n50 filename
Given a file with a list of numbers denoting contig lengths, calculate N50.
Input file can be both FASTA or a list of sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(n50.__doc__)
p.add_option(
"--print0",
default=False,
action="store_true",
help="Print size and L50 to stdout",
)
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
ctgsizes = []
# Guess file format
probe = open(args[0]).readline()[0]
isFasta = probe == ">"
if isFasta:
for filename in args:
f = Fasta(filename)
ctgsizes += list(b for a, b in f.itersizes())
else:
for row in must_open(args):
try:
ctgsize = int(float(row.split()[-1]))
except ValueError:
continue
ctgsizes.append(ctgsize)
a50, l50, nn50 = calculate_A50(ctgsizes)
sumsize = sum(ctgsizes)
minsize = min(ctgsizes)
maxsize = max(ctgsizes)
n = len(ctgsizes)
print(", ".join(args), file=sys.stderr)
summary = (sumsize, l50, nn50, minsize, maxsize, n)
print(
" ".join("{0}={1}".format(a, b) for a, b in zip(header, summary)),
file=sys.stderr,
)
loghistogram(ctgsizes)
if opts.print0:
print("\t".join(str(x) for x in (",".join(args), sumsize, l50)))
return zip(header, summary)
def n50(args):
"""
%prog n50 filename
Given a file with a list of numbers denoting contig lengths, calculate N50.
Input file can be both FASTA or a list of sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(n50.__doc__)
p.add_option(
"--print0", default=False, action="store_true", help="Print size and L50 to stdout [default: %default]"
)
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
ctgsizes = []
# Guess file format
probe = open(args[0]).readline()[0]
isFasta = probe == ">"
if isFasta:
for filename in args:
f = Fasta(filename)
ctgsizes += list(b for a, b in f.itersizes())
else:
for row in must_open(args):
try:
ctgsize = int(row.split()[-1])
except ValueError:
continue
ctgsizes.append(ctgsize)
a50, l50, nn50 = calculate_A50(ctgsizes)
sumsize = sum(ctgsizes)
minsize = min(ctgsizes)
maxsize = max(ctgsizes)
n = len(ctgsizes)
print >> sys.stderr, ", ".join(args)
summary = (sumsize, l50, nn50, minsize, maxsize, n)
print >> sys.stderr, " ".join("{0}={1}".format(a, b) for a, b in zip(header, summary))
loghistogram(ctgsizes)
if opts.print0:
print "\t".join(str(x) for x in (",".join(args), sumsize, l50))
return zip(header, summary)
def n50(args):
"""
%prog n50 filename
Given a file with a list of numbers denoting contig lengths, calculate N50.
Input file can be both FASTA or a list of sizes.
"""
p = OptionParser(n50.__doc__)
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
ctgsizes = []
# Guess file format
probe = open(args[0]).readline()[0]
isFasta = (probe == '>')
if isFasta:
for filename in args:
f = Fasta(filename)
ctgsizes += list(b for a, b in f.itersizes())
else:
for row in must_open(args):
try:
ctgsize = int(row.split()[-1])
except ValueError:
continue
ctgsizes.append(ctgsize)
a50, l50, nn50 = calculate_A50(ctgsizes)
sumsize = sum(ctgsizes)
minsize = min(ctgsizes)
maxsize = max(ctgsizes)
n = len(ctgsizes)
print >> sys.stderr, ", ".join(args)
summary = (sumsize, l50, nn50, minsize, maxsize, n)
print >> sys.stderr, " ".join("{0}={1}".format(a, b) for a, b in \
zip(header, summary))
loghistogram(ctgsizes, summary=False)
return zip(header, summary)
def summary(args):
"""
%prog summary cdhit.clstr
Parse cdhit.clstr file to get distribution of cluster sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(summary.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
clstrfile, = args
cf = ClstrFile(clstrfile)
data = list(cf.iter_sizes())
loghistogram(data, summary=True)
def summary(args):
"""
%prog summary cdhit.clstr
Parse cdhit.clstr file to get distribution of cluster sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(summary.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(clstrfile, ) = args
cf = ClstrFile(clstrfile)
data = list(cf.iter_sizes())
loghistogram(data, summary=True)
def summary(args):
"""
%prog summary cdhit.clstr
Parse cdhit.clstr file to get distribution of cluster sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(summary.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
clstrfile, = args
assert clstrfile.endswith(".clstr")
fp = open(clstrfile)
data = []
for clstr, members in read_block(fp, ">"):
size = len(members)
data.append(size)
loghistogram(data)
def summary(args):
"""
%prog summary cdhit.clstr
Parse cdhit.clstr file to get distribution of cluster sizes.
"""
from jcvi.graphics.histogram import loghistogram
p = OptionParser(summary.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
clstrfile, = args
assert clstrfile.endswith(".clstr")
fp = open(clstrfile)
data = []
for clstr, members in read_block(fp, ">"):
size = len(members)
data.append(size)
loghistogram(data)
