def count(args):
"""
%prog count cdhit.consensus.fasta
Scan the headers for the consensus clusters and count the number of reads.
"""
from jcvi.graphics.histogram import stem_leaf_plot
from jcvi.utils.cbook import SummaryStats
p = OptionParser(count.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
f = Fasta(fastafile, lazy=True)
sizes = []
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
sizes.append(1)
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
sizes.append(int(size))
s = SummaryStats(sizes)
print >> sys.stderr, s
stem_leaf_plot(s.data, 0, 100, 20, title="Cluster size")
def filter(args):
"""
%prog filter consensus.fasta
Filter consensus sequence with min cluster size.
"""
from jcvi.formats.fasta import Fasta, SeqIO
p = OptionParser(filter.__doc__)
p.add_option("--minsize", default=10, type="int",
help="Minimum cluster size")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
minsize = opts.minsize
f = Fasta(fastafile, lazy=True)
fw = must_open(opts.outfile, "w")
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
size = int(size)
if size < minsize:
continue
SeqIO.write(rec, fw, "fasta")
def count(args):
"""
%prog count cdhit.consensus.fasta
Scan the headers for the consensus clusters and count the number of reads.
"""
from jcvi.formats.fasta import Fasta
from jcvi.graphics.histogram import stem_leaf_plot
from jcvi.utils.cbook import SummaryStats
p = OptionParser(count.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
f = Fasta(fastafile, lazy=True)
sizes = []
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
sizes.append(1)
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
sizes.append(int(size))
s = SummaryStats(sizes)
print >> sys.stderr, s
stem_leaf_plot(s.data, 0, 100, 20, title="Cluster size")
def filter(args):
"""
%prog filter consensus.fasta
Filter consensus sequence with min cluster size.
"""
from jcvi.formats.fasta import Fasta, SeqIO
p = OptionParser(filter.__doc__)
p.add_option("--minsize",
default=10,
type="int",
help="Minimum cluster size")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
minsize = opts.minsize
f = Fasta(fastafile, lazy=True)
fw = must_open(opts.outfile, "w")
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
size = int(size)
if size < minsize:
continue
SeqIO.write(rec, fw, "fasta")
def filter(args):
"""
%prog filter *.consensus.fasta
Filter consensus sequence with min cluster size.
"""
from jcvi.formats.fasta import Fasta, SeqIO
p = OptionParser(filter.__doc__)
p.add_option("--minsize",
default=2,
type="int",
help="Minimum cluster size")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fastafiles = args
minsize = opts.minsize
totalreads = totalassembled = 0
fw = must_open(opts.outfile, "w")
for i, fastafile in enumerate(fastafiles):
f = Fasta(fastafile, lazy=True)
pf = "s{0:03d}".format(i)
nreads = nsingletons = nclusters = 0
for desc, rec in f.iterdescriptions_ordered():
nclusters += 1
if desc.startswith("singleton"):
nsingletons += 1
nreads += 1
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
size = int(size)
nreads += size
if size < minsize:
continue
rec.description = rec.description.split(None, 1)[-1]
rec.id = pf + "_" + rec.id
SeqIO.write(rec, fw, "fasta")
logging.debug("Scanned {0} clusters with {1} reads ..".format(
nclusters, nreads))
cclusters, creads = nclusters - nsingletons, nreads - nsingletons
logging.debug(
"Saved {0} clusters (min={1}) with {2} reads (avg:{3}) [{4}]".
format(cclusters, minsize, creads, creads / cclusters, pf))
totalreads += nreads
totalassembled += nreads - nsingletons
logging.debug("Total assembled: {0}".format(
percentage(totalassembled, totalreads)))
def filter(args):
"""
%prog filter *.consensus.fasta
Filter consensus sequence with min cluster size.
"""
from jcvi.formats.fasta import Fasta, SeqIO
p = OptionParser(filter.__doc__)
p.add_option("--minsize", default=2, type="int",
help="Minimum cluster size")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fastafiles = args
minsize = opts.minsize
totalreads = totalassembled = 0
fw = must_open(opts.outfile, "w")
for i, fastafile in enumerate(fastafiles):
f = Fasta(fastafile, lazy=True)
pf = "s{0:03d}".format(i)
nreads = nsingletons = nclusters = 0
for desc, rec in f.iterdescriptions_ordered():
nclusters += 1
if desc.startswith("singleton"):
nsingletons += 1
nreads += 1
continue
# consensus_for_cluster_0 with 63 sequences
name, w, size, seqs = desc.split()
assert w == "with"
size = int(size)
nreads += size
if size < minsize:
continue
rec.description = rec.description.split(None, 1)[-1]
rec.id = pf + "_" + rec.id
SeqIO.write(rec, fw, "fasta")
logging.debug("Scanned {0} clusters with {1} reads ..".\
format(nclusters, nreads))
cclusters, creads = nclusters - nsingletons, nreads - nsingletons
logging.debug("Saved {0} clusters (min={1}) with {2} reads (avg:{3}) [{4}]".\
format(cclusters, minsize, creads, creads / cclusters, pf))
totalreads += nreads
totalassembled += nreads - nsingletons
logging.debug("Total assembled: {0}".\
format(percentage(totalassembled, totalreads)))
def count(args):
"""
%prog count cdhit.consensus.fasta
Scan the headers for the consensus clusters and count the number of reads.
"""
from jcvi.graphics.histogram import stem_leaf_plot
from jcvi.utils.cbook import SummaryStats
p = OptionParser(count.__doc__)
p.add_option("--csv", help="Write depth per contig to file")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(fastafile, ) = args
csv = open(opts.csv, "w") if opts.csv else None
f = Fasta(fastafile, lazy=True)
sizes = []
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
sizes.append(1)
continue
# consensus_for_cluster_0 with 63 sequences
if "with" in desc:
name, w, size, seqs = desc.split()
if csv:
print("\t".join(str(x) for x in (name, size, len(rec))),
file=csv)
assert w == "with"
sizes.append(int(size))
# MRD85:00603:02472;size=167;
else:
name, size, tail = desc.split(";")
sizes.append(int(size.replace("size=", "")))
if csv:
csv.close()
logging.debug("File written to `%s`.", opts.csv)
s = SummaryStats(sizes)
print(s, file=sys.stderr)
stem_leaf_plot(s.data, 0, 100, 20, title="Cluster size")
def count(args):
"""
%prog count cdhit.consensus.fasta
Scan the headers for the consensus clusters and count the number of reads.
"""
from jcvi.graphics.histogram import stem_leaf_plot
from jcvi.utils.cbook import SummaryStats
p = OptionParser(count.__doc__)
p.add_option("--csv", help="Write depth per contig to file")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
csv = open(opts.csv, "w") if opts.csv else None
f = Fasta(fastafile, lazy=True)
sizes = []
for desc, rec in f.iterdescriptions_ordered():
if desc.startswith("singleton"):
sizes.append(1)
continue
# consensus_for_cluster_0 with 63 sequences
if "with" in desc:
name, w, size, seqs = desc.split()
if csv:
print("\t".join(str(x)
for x in (name, size, len(rec))), file=csv)
assert w == "with"
sizes.append(int(size))
# MRD85:00603:02472;size=167;
else:
name, size, tail = desc.split(";")
sizes.append(int(size.replace("size=", "")))
if csv:
csv.close()
logging.debug("File written to `{0}`".format(opts.csv))
s = SummaryStats(sizes)
print(s, file=sys.stderr)
stem_leaf_plot(s.data, 0, 100, 20, title="Cluster size")
