def prepare(args):
"""
%prog prepare *.fastq
Generate run.sh script to run clc_novo_assemble.
"""
from itertools import groupby
from jcvi.utils.iter import grouper
from jcvi.formats.base import check_exists
from jcvi.assembly.base import FastqNamings, Library
p = OptionParser(prepare.__doc__ + FastqNamings)
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)
library_name = lambda x: "-".join(\
op.basename(x).split(".")[0].split("-")[:2])
libs = [(Library(x), sorted(fs)) for x, fs in \
groupby(fnames, key=library_name)]
libs.sort(key=lambda x: x[0].size)
singletons = []
pairs = []
write_file("license.properties", CLCLICENSE)
for lib, fs in libs:
size = lib.size
stddev = lib.stddev
if size == 0:
singletons += fs
continue
for f in fs:
reverse_seq = 0 if ".corr." in f else lib.reverse_seq
fb = "bf" if reverse_seq else "fb"
minsize, maxsize = size - 2 * stddev, size + 2 * stddev
pair_opt = "-p {0} ss {1} {2} ".format(fb, minsize, maxsize)
if ".1." in f:
f = f.replace(".1.", ".?.")
pairs.append(pair_opt + "-i {0}".format(f))
elif ".2." in f:
continue
else:
pairs.append(pair_opt + f)
cmd = "clc_novo_assemble --cpus 32 -o contigs.fasta \\\n"
cmd += "\t-q {0} \\\n".format(" ".join(singletons))
cmd += "\n".join("\t{0} \\".format(x) for x in pairs)
runfile = "run.sh"
if check_exists(runfile):
fw = open(runfile, "w")
print >> fw, "#!/bin/bash\n"
print >> fw, cmd
logging.debug("Run script written to `{0}`.".format(runfile))
def prepare(args):
"""
%prog prepare *.fastq
Scan input fastq files (see below) and write SOAP config files based
on inputfiles.
"""
from jcvi.utils.iter import grouper
from jcvi.formats.base import check_exists
p = OptionParser(prepare.__doc__ + FastqNamings)
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)
cfgfile = "soap.config"
fw = open(cfgfile, "w")
library_name = lambda x: "-".join(\
op.basename(x).split(".")[0].split("-")[:2])
libs = [(Library(x), sorted(fs)) for x, fs in \
groupby(fnames, key=library_name)]
libs.sort(key=lambda x: x[0].size)
rank = 0
singletons = []
for lib, fs in libs:
size = lib.size
if size == 0:
singletons = fs
continue
rank += 1
block = "[LIB]\n"
block += "avg_ins={0}\n".format(size)
f = fs[0]
reverse_seq = 0 if ".corr." in f else lib.reverse_seq
block += "reverse_seq={0}\n".format(reverse_seq)
block += "asm_flags={0}\n".format(lib.asm_flags)
block += "rank={0}\n".format(rank)
if singletons:
fs += singletons
singletons = []
for f in fs:
if ".1." in f:
tag = "q1"
elif ".2." in f:
tag = "q2"
else:
tag = "q"
block += "{0}={1}\n".format(tag, f)
print >> sys.stderr, block
print >> fw, block
runfile = "run.sh"
if check_exists(runfile):
fw = open(runfile, "w")
print >> fw, SOAPRUN
logging.debug("Run script written to `{0}`.".format(runfile))
def prepare(args):
"""
%prog prepare *.fastq
Scan input fastq files (see below) and write SOAP config files based
on inputfiles.
"""
from jcvi.utils.iter import grouper
from jcvi.formats.base import check_exists
p = OptionParser(prepare.__doc__ + FastqNamings)
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)
cfgfile = "soap.config"
fw = open(cfgfile, "w")
library_name = lambda x: "-".join(\
op.basename(x).split(".")[0].split("-")[:2])
libs = [(Library(x), sorted(fs)) for x, fs in \
groupby(fnames, key=library_name)]
libs.sort(key=lambda x: x[0].size)
rank = 0
singletons = []
for lib, fs in libs:
size = lib.size
if size == 0:
singletons = fs
continue
rank += 1
block = "[LIB]\n"
block += "avg_ins={0}\n".format(size)
f = fs[0]
reverse_seq = 0 if ".corr." in f else lib.reverse_seq
block += "reverse_seq={0}\n".format(reverse_seq)
block += "asm_flags={0}\n".format(lib.asm_flags)
block += "rank={0}\n".format(rank)
if singletons:
fs += singletons
singletons = []
for f in fs:
if ".1." in f:
tag = "q1"
elif ".2." in f:
tag = "q2"
else:
tag = "q"
block += "{0}={1}\n".format(tag, f)
print >> sys.stderr, block
print >> fw, block
runfile = "run.sh"
if check_exists(runfile):
fw = open(runfile, "w")
print >> fw, SOAPRUN
logging.debug("Run script written to `{0}`.".format(runfile))
def prepare(args):
"""
%prog prepare "B. oleracea" *.fastq
Scan input fastq files (see below) and create `in_groups.csv` and
`in_libs.csv`. The species name does not really matter.
"""
from jcvi.utils.table import write_csv
from jcvi.formats.base import check_exists
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("--norun", default=False, action="store_true",
help="Don't write `run.sh` script [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
organism_name = args[0]
project_name = "".join(x[0] for x in organism_name.split()).upper()
fnames = sorted(glob("*.fastq*") if len(args) == 1 else args[1:])
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
groupheader = "group_name library_name file_name".split()
libheader = "library_name project_name organism_name type paired "\
"frag_size frag_stddev insert_size insert_stddev read_orientation "\
"genomic_start genomic_end".split()
groupcontents = []
libs = []
for file_name in fnames:
group_name = op.basename(file_name).split(".")[0]
library_name = "-".join(group_name.split("-")[:2])
# Handle paired files and convert to wildcard
if ".1." in file_name:
file_name = file_name.replace(".1.", ".?.")
elif ".2." in file_name:
continue
groupcontents.append((group_name, library_name, file_name))
if library_name not in libs:
libs.append(library_name)
libcontents = []
for library_name in libs:
L = Library(library_name)
size = L.size
stddev = L.stddev
type = L.type
paired = L.paired
read_orientation = L.read_orientation
size = size or ""
stddev = stddev or ""
frag_size = size if type == "fragment" else ""
frag_stddev = stddev if type == "fragment" else ""
insert_size = size if type != "fragment" else ""
insert_stddev = stddev if type != "fragment" else ""
genomic_start, genomic_end = "", ""
libcontents.append((library_name, project_name, organism_name, type, \
paired, frag_size, frag_stddev, insert_size, insert_stddev, \
read_orientation, genomic_start, genomic_end))
write_csv(groupheader, groupcontents, filename="in_groups.csv", tee=True)
logging.debug("`in_group.csv` created (# of groups = {0}).".\
format(len(groupcontents)))
write_csv(libheader, libcontents, filename="in_libs.csv", tee=True)
logging.debug("`in_libs.csv` created (# of libs = {0}).".\
format(len(libcontents)))
runfile = "run.sh"
if not opts.norun and check_exists(runfile):
fw = open(runfile, "w")
print >> fw, ALLPATHSRUN
logging.debug("Run script written to `{0}`.".format(runfile))
def prepare(args):
"""
%prog prepare "B. oleracea" *.fastq
Scan input fastq files (see below) and create `in_groups.csv` and
`in_libs.csv`. The species name does not really matter.
"""
from jcvi.utils.table import write_csv
from jcvi.formats.base import check_exists
p = OptionParser(prepare.__doc__ + FastqNamings)
p.add_option("--norun", default=False, action="store_true",
help="Don't write `run.sh` script [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
organism_name = args[0]
project_name = "".join(x[0] for x in organism_name.split()).upper()
fnames = sorted(glob("*.fastq*") if len(args) == 1 else args[1:])
for x in fnames:
assert op.exists(x), "File `{0}` not found.".format(x)
groupheader = "group_name library_name file_name".split()
libheader = "library_name project_name organism_name type paired "\
"frag_size frag_stddev insert_size insert_stddev read_orientation "\
"genomic_start genomic_end".split()
groupcontents = []
libs = []
for file_name in fnames:
group_name = op.basename(file_name).split(".")[0]
library_name = "-".join(group_name.split("-")[:2])
# Handle paired files and convert to wildcard
if ".1." in file_name:
file_name = file_name.replace(".1.", ".?.")
elif ".2." in file_name:
continue
groupcontents.append((group_name, library_name, file_name))
if library_name not in libs:
libs.append(library_name)
libcontents = []
for library_name in libs:
L = Library(library_name)
size = L.size
stddev = L.stddev
type = L.type
paired = L.paired
read_orientation = L.read_orientation
size = size or ""
stddev = stddev or ""
frag_size = size if type == "fragment" else ""
frag_stddev = stddev if type == "fragment" else ""
insert_size = size if type != "fragment" else ""
insert_stddev = stddev if type != "fragment" else ""
genomic_start, genomic_end = "", ""
libcontents.append((library_name, project_name, organism_name, type, \
paired, frag_size, frag_stddev, insert_size, insert_stddev, \
read_orientation, genomic_start, genomic_end))
write_csv(groupheader, groupcontents, filename="in_groups.csv", tee=True)
logging.debug("`in_group.csv` created (# of groups = {0}).".\
format(len(groupcontents)))
write_csv(libheader, libcontents, filename="in_libs.csv", tee=True)
logging.debug("`in_libs.csv` created (# of libs = {0}).".\
format(len(libcontents)))
runfile = "run.sh"
if not opts.norun and check_exists(runfile):
fw = open(runfile, "w")
print >> fw, ALLPATHSRUN
logging.debug("Run script written to `{0}`.".format(runfile))