def prepare(args):
"""
%prog prepare genomesize *.fastq
Prepare MERACULOUS configuation file. Genome size should be entered in Mb.
"""
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("-K", default=51, type="int", help="K-mer size")
p.set_cpus(cpus=32)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
genomesize = float(args[0]) / 1000
fnames = args[1:]
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
s = comment_banner("Meraculous params file") + "\n"
s += comment_banner("Basic parameters") + "\n"
s += "# Describe the libraries ( one line per library )\n"
s += "# " + " ".join(header.split()) + "\n"
libs = get_libs(fnames)
lib_seqs = []
rank = 0
for lib, fs in libs:
size = lib.size
if size == 0:
continue
rank += 1
library_name = lib.library_name
name = library_name.replace("-", "")
wildcard = "{0}*.1.*,{0}*.2.*".format(library_name)
rl = max(readlen([x]) for x in fs)
lib_seq = lib.get_lib_seq(wildcard, name, rl, rank)
lib_seqs.append(lib_seq)
s += "\n" + "\n".join(load_csv(None, lib_seqs, sep=" ")) + "\n"
params = [("genome_size", genomesize),
("is_diploid", 0),
("mer_size", opts.K),
("num_prefix_blocks", 1),
("no_read_validation", 0),
("local_num_procs", opts.cpus)]
s += "\n" + "\n".join(load_csv(None, params, sep=" ")) + "\n"
cfgfile = "meraculous.config"
write_file(cfgfile, s, tee=True)
s = "~/export/meraculous/bin/run_meraculous.sh -c {0}"\
.format(cfgfile)
runsh = "run.sh"
write_file(runsh, s)
def prepare(args):
"""
%prog prepare genomesize *.fastq
Prepare MERACULOUS configuation file. Genome size should be entered in Mb.
"""
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("-K", default=51, type="int", help="K-mer size")
p.set_cpus(cpus=32)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
genomesize = float(args[0]) / 1000
fnames = args[1:]
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
s = comment_banner("Meraculous params file") + "\n"
s += comment_banner("Basic parameters") + "\n"
s += "# Describe the libraries ( one line per library )\n"
s += "# " + " ".join(header.split()) + "\n"
libs = get_libs(fnames)
lib_seqs = []
rank = 0
for lib, fs in libs:
size = lib.size
if size == 0:
continue
rank += 1
library_name = lib.library_name
name = library_name.replace("-", "")
wildcard = "{0}*.1.*,{0}*.2.*".format(library_name)
rl = max(readlen([x]) for x in fs)
lib_seq = lib.get_lib_seq(wildcard, name, rl, rank)
lib_seqs.append(lib_seq)
s += "\n" + "\n".join(load_csv(None, lib_seqs, sep=" ")) + "\n"
params = [("genome_size", genomesize), ("is_diploid", 0),
("mer_size", opts.K), ("num_prefix_blocks", 1),
("no_read_validation", 0), ("local_num_procs", opts.cpus)]
s += "\n" + "\n".join(load_csv(None, params, sep=" ")) + "\n"
cfgfile = "meraculous.config"
write_file(cfgfile, s, tee=True)
s = "~/export/meraculous/bin/run_meraculous.sh -c {0}"\
.format(cfgfile)
runsh = "run.sh"
write_file(runsh, s)
def write_libraries(fastqs, aligner=None):
from jcvi.assembly.base import get_libs
libs = get_libs(fastqs)
assert libs
libtxt = "libraries.txt"
contents = []
for i, (lib, fns) in enumerate(libs):
fns = " ".join(fns)
pe = "RF" if lib.read_orientation == "outward" else "FR"
cc = ["lib{0}".format(i + 1), fns, lib.size, 0.75, pe]
if aligner:
cc.insert(1, aligner)
libline = " ".join(str(x) for x in cc)
contents.append(libline)
write_file(libtxt, "\n".join(contents), tee=True)
return libtxt
def prepare(args):
"""
%prog prepare *.fastq
Scan input fastq files (see below) and write SOAP config files based
on inputfiles. Use "--scaffold contigs.fasta" to perform scaffolding.
"""
from jcvi.formats.base import write_file
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("-K", default=45, type="int", help="K-mer size [default: %default]")
p.add_option(
"--assemble_1st_rank_only",
default=False,
action="store_true",
help="Assemble the first rank only, other libs asm_flags=2 [default: %default]",
)
p.add_option("--scaffold", help="Only perform scaffolding [default: %default]")
p.add_option("--gapclose", help="Only perform gap closure [default: %default]")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fnames = args
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
a1st = opts.assemble_1st_rank_only
cfgfile = "soap.config"
gc_cfgfile = "soap.gc.config"
fw = open(cfgfile, "w")
fw_gc = open(gc_cfgfile, "w")
libs = get_libs(fnames)
rank = 0
singletons = []
max_rd_len = max(readlen([f]) for f in fnames)
block = "max_rd_len={0}\n".format(max_rd_len)
for stream in (sys.stderr, fw, fw_gc):
print >> stream, block
# Collect singletons first
singletons = []
for lib, fs in libs:
if lib.size == 0:
singletons += fs
continue
for lib, fs in libs:
size = lib.size
if size == 0:
continue
rank += 1
block = "[LIB]\n"
block += "avg_ins={0}\n".format(size)
f = fs[0]
block += "reverse_seq={0}\n".format(lib.reverse_seq)
asm_flags = 2 if (rank > 1 and a1st) else lib.asm_flags
block += "asm_flags={0}\n".format(asm_flags)
block += "rank={0}\n".format(rank)
if lib.reverse_seq:
pair_num_cutoff = 3
block += "pair_num_cutoff={0}\n".format(pair_num_cutoff)
block += "map_len=35\n"
for f in fs:
if ".1." in f:
tag = "q1"
elif ".2." in f:
tag = "q2"
block += "{0}={1}\n".format(tag, f)
if rank == 1:
for s in singletons:
block += "q={0}\n".format(s)
print >>sys.stderr, block
print >> fw, block
if asm_flags > 2:
print >> fw_gc, block
runfile = "run.sh"
scaffold = opts.scaffold
header = SOAPHEADER.format(opts.cpus, opts.K)
if opts.gapclose:
gapclose = opts.gapclose
outfile = gapclose.rsplit(".", 1)[0] + ".closed.fasta"
template = header + GCRUNG.format(gapclose, outfile)
else:
template = header + (SCFRUN % scaffold if scaffold else SOAPRUN)
write_file(runfile, template, meta="run script")
fw.close()
fw_gc.close()
def prepare(args):
"""
%prog prepare *.fastq
Scan input fastq files (see below) and write SOAP config files based
on inputfiles. Use "--scaffold contigs.fasta" to perform scaffolding.
"""
from jcvi.formats.base import write_file
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("-K",
default=45,
type="int",
help="K-mer size [default: %default]")
p.add_option(
"--assemble_1st_rank_only",
default=False,
action="store_true",
help=
"Assemble the first rank only, other libs asm_flags=2 [default: %default]"
)
p.add_option("--scaffold",
help="Only perform scaffolding [default: %default]")
p.add_option("--gapclose",
help="Only perform gap closure [default: %default]")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fnames = args
K = opts.K
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
a1st = opts.assemble_1st_rank_only
cfgfile = "soap.config"
gc_cfgfile = "soap.gc.config"
fw = open(cfgfile, "w")
fw_gc = open(gc_cfgfile, "w")
libs = get_libs(fnames)
rank = 0
singletons = []
max_rd_len = max(readlen([f]) for f in fnames)
block = "max_rd_len={0}\n".format(max_rd_len)
for stream in (sys.stderr, fw, fw_gc):
print(block, file=stream)
# Collect singletons first
singletons = []
for lib, fs in libs:
if lib.size == 0:
singletons += fs
continue
for lib, fs in libs:
size = lib.size
if size == 0:
continue
rank += 1
block = "[LIB]\n"
block += "avg_ins={0}\n".format(size)
f = fs[0]
block += "reverse_seq={0}\n".format(lib.reverse_seq)
asm_flags = 2 if (rank > 1 and a1st) else lib.asm_flags
block += "asm_flags={0}\n".format(asm_flags)
block += "rank={0}\n".format(rank)
if lib.reverse_seq:
pair_num_cutoff = 3
block += "pair_num_cutoff={0}\n".format(pair_num_cutoff)
block += "map_len=35\n"
for f in fs:
if ".1." in f:
tag = "q1"
elif ".2." in f:
tag = "q2"
block += "{0}={1}\n".format(tag, f)
if rank == 1:
for s in singletons:
tag = "q" if is_fastq(s) else "f"
block += tag + "={0}\n".format(s)
print(block, file=sys.stderr)
print(block, file=fw)
if asm_flags > 2:
print(block, file=fw_gc)
runfile = "run.sh"
scaffold = opts.scaffold
bb = 63 if K <= 63 else 127
binary = "SOAPdenovo-{0}mer".format(bb)
header = SOAPHEADER.format(opts.cpus, K, binary)
if opts.gapclose:
gapclose = opts.gapclose
outfile = gapclose.rsplit(".", 1)[0] + ".closed.fasta"
template = header + GCRUNG.format(gapclose, outfile)
else:
template = header + (SCFRUN % scaffold if scaffold else SOAPRUN)
write_file(runfile, template)
fw.close()
fw_gc.close()
