def aln(args):
"""
%prog aln database.fasta *.fastq
Wrapper for `bwa aln` except this will run over a set of files.
"""
p = OptionParser(aln.__doc__)
p.add_option("--cpus",
default=32,
help="Number of cpus to use [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, readfiles = args[0], args[1:]
safile = check_index(dbfile, grid=grid)
for readfile in readfiles:
saifile = check_aln(dbfile, readfile, grid=grid, cpus=opts.cpus)
def bwasw(args):
"""
%prog bwasw database.fasta long_read.fastq
Wrapper for `bwa bwasw`. Output will be long_read.sam.
"""
p = OptionParser(bwasw.__doc__)
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, readfile = args
safile = check_index(dbfile, grid=grid)
saifile = check_aln(dbfile, readfile, grid=grid)
samfile = readfile.rsplit(".", 1)[0] + ".sam"
if op.exists(samfile):
logging.error("`{0}` exists. `bwa bwasw` already run.".format(samfile))
return
cmd = "bwa bwasw -t 32 {0} {1} ".format(dbfile, readfile)
cmd += "{0}".format(extra)
sh(cmd, grid=grid, outfile=samfile)
def bwasw(args):
"""
%prog bwasw database.fasta long_read.fastq
Wrapper for `bwa bwasw`. Output will be long_read.sam.
"""
p = OptionParser(bwasw.__doc__)
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, readfile = args
safile = check_index(dbfile, grid=grid)
saifile = check_aln(dbfile, readfile, grid=grid)
samfile = readfile.rsplit(".", 1)[0] + ".sam"
if op.exists(samfile):
logging.error("`{0}` exists. `bwa bwasw` already run.".format(samfile))
return
cmd = "bwa bwasw -t 32 {0} {1} ".format(dbfile, readfile)
cmd += "{0}".format(extra)
sh(cmd, grid=grid, outfile=samfile)
def map(args):
"""
%prog map reference fastqfiles
Use `clc_ref_assemble` to map the read files to a reference. Use a non-zero
-s option to turn on paired end mode.
"""
p = OptionParser(map.__doc__)
p.add_option("-o", dest="outfile", default=None,
help="Output prefix.cas file [default: %default]")
p.add_option("-s", dest="size", default=0, type="int",
help="Use paired end mapping with insert [default: %default]")
p.add_option("--short", default=False, action="store_true",
help="Use `clc_ref_assemble_short` as the mapper [default: %default]")
p.add_option("--orientations", default="fb",
help="The reads have the orientations [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
license = "license.properties"
if not op.exists(license):
sh("cp ~/{0} .".format(license))
ref = args[0]
assert op.exists(ref)
fastqfiles = args[1:]
size = opts.size
orientations = opts.orientations
assert orientations in ("fb", "bf", "ff", "bb")
cmd = "clc_ref_assemble_short" if opts.short else "clc_ref_assemble_long"
readprefix = op.basename(fastqfiles[0]).split(".", 1)[0]
refprefix = op.basename(ref).split(".", 1)[0]
outfile = opts.outfile or "{0}.{1}".format(readprefix, refprefix)
if not outfile.endswith(".cas"):
outfile += ".cas"
cmd += " --cpus 16"
cmd += " -d {0} -o {1} -q ".format(ref, outfile)
fastqs = " ".join(fastqfiles)
if size == 0:
cmd += fastqs
else:
assert len(fastqfiles) == 2
stddev = size / 4
lb, ub = size - stddev, size + stddev
cmd += " -p {0} ss {1} {2} -i {3} ".format(orientations, lb, ub, fastqs)
if opts.extra:
cmd += " " + opts.extra
if not opts.short:
cmd += " -l 0.8 -s 0.98"
sh(cmd, grid=opts.grid)
def map(args):
"""
%prog map reference fastqfiles
Use `clc_ref_assemble` to map the read files to a reference. Use a non-zero
-s option to turn on paired end mode.
"""
p = OptionParser(map.__doc__)
p.add_option("-o", dest="outfile", default=None,
help="Output prefix.cas file [default: %default]")
p.add_option("-s", dest="size", default=0, type="int",
help="Use paired end mapping with insert [default: %default]")
p.add_option("--short", default=False, action="store_true",
help="Use `clc_ref_assemble_short` as the mapper [default: %default]")
p.add_option("--orientations", default="fb",
help="The reads have the orientations [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(not p.print_help())
write_file("license.properties", CLCLICENSE)
ref = args[0]
assert op.exists(ref)
fastqfiles = args[1:]
size = opts.size
orientations = opts.orientations
assert orientations in ("fb", "bf", "ff", "bb")
cmd = "clc_ref_assemble_short" if opts.short else "clc_ref_assemble_long"
readprefix = op.basename(fastqfiles[0]).split(".", 1)[0]
refprefix = op.basename(ref).split(".", 1)[0]
outfile = opts.outfile or "{0}.{1}".format(readprefix, refprefix)
if not outfile.endswith(".cas"):
outfile += ".cas"
cmd += " --cpus 16"
cmd += " -d {0} -o {1} -q ".format(ref, outfile)
fastqs = " ".join(fastqfiles)
if size == 0:
cmd += fastqs
else:
assert len(fastqfiles) == 2
stddev = size / 4
lb, ub = size - stddev, size + stddev
cmd += " -p {0} ss {1} {2} -i {3} ".format(orientations, lb, ub, fastqs)
if opts.extra:
cmd += " " + opts.extra
if not opts.short:
cmd += " -l 0.8 -s 0.98"
sh(cmd, grid=opts.grid)
def sampe(args):
"""
%prog sampe database.fasta read1.fq read2.fq
Wrapper for `bwa sampe`. Output will be read1.sam.
"""
p = OptionParser(sampe.__doc__)
p.add_option("--bam",
default=False,
action="store_true",
help="write to bam file [default: %default]")
p.add_option("--cpus",
default=32,
help="Number of cpus to use [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, read1file, read2file = args
safile = check_index(dbfile, grid=grid)
sai1file = check_aln(dbfile, read1file, grid=grid, cpus=opts.cpus)
sai2file = check_aln(dbfile, read2file, grid=grid, cpus=opts.cpus)
prefix = read1file.rsplit(".", 1)[0]
samfile = (prefix + ".bam") if opts.bam else (prefix + ".sam")
if op.exists(samfile):
logging.error("`{0}` exists. `bwa samse` already run.".format(samfile))
return
cmd = "bwa sampe {0} {1} {2} {3} {4} ".format(dbfile, sai1file, sai2file,
read1file, read2file)
cmd += "{0}".format(extra)
if opts.bam:
cmd += " | samtools view -bS -F 4 - "
sh(cmd, grid=grid, outfile=samfile)
def index(args):
"""
%prog index database.fasta
Wrapper for `bwa index`. Same interface, only adds grid submission.
"""
p = OptionParser(index.__doc__)
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, = args
safile = check_index(dbfile, grid=grid)
def index(args):
"""
%prog index database.fasta
Wrapper for `bwa index`. Same interface, only adds grid submission.
"""
p = OptionParser(index.__doc__)
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, = args
safile = check_index(dbfile, grid=grid)
def sampe(args):
"""
%prog sampe database.fasta read1.fq read2.fq
Wrapper for `bwa sampe`. Output will be read1.sam.
"""
p = OptionParser(sampe.__doc__)
p.add_option("--bam", default=False, action="store_true",
help="write to bam file [default: %default]")
p.add_option("--cpus", default=32,
help="Number of cpus to use [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, read1file, read2file = args
safile = check_index(dbfile, grid=grid)
sai1file = check_aln(dbfile, read1file, grid=grid, cpus=opts.cpus)
sai2file = check_aln(dbfile, read2file, grid=grid, cpus=opts.cpus)
prefix = read1file.rsplit(".", 1)[0]
samfile = (prefix + ".bam") if opts.bam else (prefix + ".sam")
if op.exists(samfile):
logging.error("`{0}` exists. `bwa samse` already run.".format(samfile))
return
cmd = "bwa sampe {0} {1} {2} {3} {4} ".format(dbfile, sai1file, sai2file,
read1file, read2file)
cmd += "{0}".format(extra)
if opts.bam:
cmd += " | samtools view -bS -F 4 - "
sh(cmd, grid=grid, outfile=samfile)
def aln(args):
"""
%prog aln database.fasta *.fastq
Wrapper for `bwa aln` except this will run over a set of files.
"""
p = OptionParser(aln.__doc__)
p.add_option("--cpus", default=32,
help="Number of cpus to use [default: %default]")
set_params(p)
set_grid(p)
opts, args = p.parse_args(args)
if len(args) < 2:
sys.exit(p.print_help())
extra = opts.extra
grid = opts.grid
dbfile, readfiles = args[0], args[1:]
safile = check_index(dbfile, grid=grid)
for readfile in readfiles:
saifile = check_aln(dbfile, readfile, grid=grid, cpus=opts.cpus)
def main():
"""
%prog database.fa query.fa [options]
Run LASTZ similar to the BLAST interface, and generates -m8 tabular format
"""
p = OptionParser(main.__doc__)
supported_formats = tuple(x.strip() for x in \
"lav, lav+text, axt, axt+, maf, maf+, maf-, sam, softsam, "\
"sam-, softsam-, cigar, BLASTN, BLASTN-, differences, rdotplot, text".split(','))
p.add_option("-a", "-A", dest="cpus", default=1, type="int",
help="parallelize job to multiple cpus [default: %default]")
p.add_option("--format", default="BLASTN-", choices=supported_formats,
help="output format, one of {0} [default: %default]".\
format("|".join(supported_formats)))
p.add_option("--path", dest="lastz_path", default=None,
help="specify LASTZ path")
p.add_option("--mask", dest="mask", default=False, action="store_true",
help="treat lower-case letters as mask info [default: %default]")
set_params(p)
set_outfile(p)
set_grid(p)
opts, args = p.parse_args()
if len(args) != 2:
sys.exit(p.print_help())
bfasta_fn, afasta_fn = args
for fn in (afasta_fn, bfasta_fn):
assert op.exists(fn)
afasta_fn = op.abspath(afasta_fn)
bfasta_fn = op.abspath(bfasta_fn)
out_fh = must_open(opts.outfile, "w")
grid = opts.grid
if grid:
print >>sys.stderr, "Running jobs on JCVI grid"
extra = opts.extra
lastz_bin = opts.lastz_path or "lastz"
assert lastz_bin.endswith("lastz"), "You need to include lastz in your path"
mask = opts.mask
cpus = opts.cpus
logging.debug("Dispatch job to %d cpus" % cpus)
format = opts.format
blastline = (format == "BLASTN-")
# The axt, maf, etc. format can only be run on splitted database (i.e. one
# FASTA record per file). The splitted files are then parallelized for the
# computation, as opposed to splitting queries through "subsample".
outdir = "outdir"
if not blastline:
from jcvi.formats.fasta import Fasta
from jcvi.formats.chain import faToTwoBit
mkdir(outdir)
bfasta_2bit = faToTwoBit(bfasta_fn)
bids = list(Fasta(bfasta_fn, lazy=True).iterkeys_ordered())
apf = op.basename(afasta_fn).split(".")[0]
args = []
# bfasta_fn, afasta_fn, outfile, lastz_bin, extra, mask, format
for id in bids:
bfasta = "/".join((bfasta_2bit, id))
outfile = op.join(outdir, "{0}.{1}.{2}".format(apf, id, format))
args.append((bfasta, afasta_fn, outfile, \
lastz_bin, extra, mask, format, grid))
if grid:
cmds = [lastz_2bit(x) for x in args]
g = Grid(cmds)
g.run()
g.writestatus()
p = Pool(cpus)
p.map(lastz_2bit, args)
return
lock = Lock()
if grid:
cmds = [lastz(k + 1, cpus, bfasta_fn, afasta_fn, out_fh, \
lock, lastz_bin, extra, mask, grid) for k in xrange(cpus)]
mkdir(outdir)
g = Grid(cmds, outfiles=[op.join(outdir, "out.{0}.lastz").\
format(i) for i in range(len(cmds))])
g.run()
g.writestatus()
else:
args = [(k + 1, cpus, bfasta_fn, afasta_fn, out_fh,
lock, lastz_bin, extra, mask) for k in xrange(cpus)]
g = Jobs(target=lastz, args=args)
g.run()
def assemble(args):
"""
Run `cap3` on a single multi FASTA file containing reads or a folder containing several
multi FASTA files. Allows for tweaking of `cap3` parameters max_gap_len, ovl_pct_id, etc.
"""
p = OptionParser(assemble.__doc__)
g1 = OptionGroup(p, "Input file options (required)",
"Note: Please choose from and provide values for one of the following parameters")
g1.add_option("--input_file", default=None,
help="input file of reads [default: %default]")
g1.add_option("--input_folder", default=None,
help="input folder containing multi FASTA files of reads [default: %default]")
g1.add_option("--input_file_list", default=None,
help="list file containing paths to multi FASTA files of reads [default: %default]")
p.add_option_group(g1)
g2 = OptionGroup(p, "Optional parameters",
"Note: If not specified, `cap3` defaults will be used")
g2.add_option("-f", "--max_gap_len", default=20, type="int",
help="maximum gap length in any overlap [default: %default]\n" +\
"Same as cap3 `-f` parameter.")
g2.add_option("-p", "--ovl_pct_id", default=90, type="int",
help="overlap percent identity cutoff [default: %default]\n" +\
"Same as cap3 `-p` parameter.")
g2.add_option("-s", "--ovl_sim_score", default=900, type="int",
help="overlap similarity score cutoff [default: %default]\n" +\
"Same as cap3 `-s` parameter.")
g2.add_option("-x", "--prefix", dest="prefix", default="cap3",
help="prefix string for output file name [default: %default]")
p.add_option_group(g2)
set_grid(p)
set_params(p)
opts, args = p.parse_args(args)
if opts.max_gap_len and opts.max_gap_len <= 1:
logging.error("--max_gap_len should be > 1")
sys.exit()
elif opts.ovl_pct_id and opts.ovl_pct_id <= 65:
logging.error("--ovl_pct_id should be > 65")
sys.exit()
elif opts.ovl_sim_score and opts.ovl_sim_score <= 250:
logging.error("--ovl_sim_score should be > 250")
sys.exit()
file_list = []
if opts.input_file_list:
if not op.isfile(opts.input_file_list):
logging.error("Input file list {0} does not exist".format(opts.input_file_list))
sys.exit()
with open(opts.input_file_list, 'r') as f:
file_list = f.read().splitlines()
elif opts.input_folder:
if not op.isdir(opts.input_folder):
logging.error("Input folder {0} does not exist".format(opts.input_folder))
sys.exit()
file_list = [file for file in os.listdir(opts.input_folder) \
if file.lower().endswith('.fa') or file.lower().endswith('.fasta')]
folder = opts.input_folder
folder = folder.rstrip('/')
for i in xrange(len(file_list)):
file_list[i] = folder + "/" + file_list[i]
elif opts.input_file:
file_list.append(opts.input_file)
else:
logging.error("Please specify one of the options for input files")
sys.exit(not p.print_help())
if len(file_list) == 0:
logging.warning("List of files to process is empty. Please check your input!")
sys.exit()
for file in file_list:
if not op.isfile(file):
logging.warning("Input file {0} does not exist".format(file))
else:
cmd = "cap3 {0} -f {1} -p {2} -s {3} -x {4}".format(file, opts.max_gap_len, \
opts.ovl_pct_id, opts.ovl_sim_score, opts.prefix)
if opts.extra:
cmd += " {0}".format(opts.extra)
logfile = "{0}.{1}.log".format(file, opts.prefix)
sh(cmd, outfile=logfile, grid=opts.grid)
def main():
"""
%prog database.fa query.fa [options]
Run LASTZ similar to the BLAST interface, and generates -m8 tabular format
"""
p = OptionParser(main.__doc__)
supported_formats = tuple(x.strip() for x in \
"lav, lav+text, axt, axt+, maf, maf+, maf-, sam, softsam, "\
"sam-, softsam-, cigar, BLASTN, BLASTN-, differences, rdotplot, text".split(','))
p.add_option("-a",
"-A",
dest="cpus",
default=1,
type="int",
help="parallelize job to multiple cpus [default: %default]")
p.add_option("--format", default="BLASTN-", choices=supported_formats,
help="output format, one of {0} [default: %default]".\
format("|".join(supported_formats)))
p.add_option("--path",
dest="lastz_path",
default=None,
help="specify LASTZ path")
p.add_option(
"--mask",
dest="mask",
default=False,
action="store_true",
help="treat lower-case letters as mask info [default: %default]")
p.add_option(
"--similar",
default=False,
action="store_true",
help="Use options tuned for close comparison [default: %default]")
set_params(p)
set_outfile(p)
set_grid(p)
opts, args = p.parse_args()
if len(args) != 2:
sys.exit(p.print_help())
bfasta_fn, afasta_fn = args
for fn in (afasta_fn, bfasta_fn):
assert op.exists(fn)
afasta_fn = op.abspath(afasta_fn)
bfasta_fn = op.abspath(bfasta_fn)
out_fh = must_open(opts.outfile, "w")
grid = opts.grid
if grid:
print >> sys.stderr, "Running jobs on JCVI grid"
extra = opts.extra
if opts.similar:
extra += similarOptions
lastz_bin = opts.lastz_path or "lastz"
assert lastz_bin.endswith(
"lastz"), "You need to include lastz in your path"
mask = opts.mask
cpus = opts.cpus
logging.debug("Dispatch job to %d cpus" % cpus)
format = opts.format
blastline = (format == "BLASTN-")
# The axt, maf, etc. format can only be run on splitted database (i.e. one
# FASTA record per file). The splitted files are then parallelized for the
# computation, as opposed to splitting queries through "subsample".
outdir = "outdir"
if not blastline:
from jcvi.formats.fasta import Fasta
from jcvi.formats.chain import faToTwoBit
mkdir(outdir)
bfasta_2bit = faToTwoBit(bfasta_fn)
bids = list(Fasta(bfasta_fn, lazy=True).iterkeys_ordered())
apf = op.basename(afasta_fn).split(".")[0]
args = []
# bfasta_fn, afasta_fn, outfile, lastz_bin, extra, mask, format
for id in bids:
bfasta = "/".join((bfasta_2bit, id))
outfile = op.join(outdir, "{0}.{1}.{2}".format(apf, id, format))
args.append((bfasta, afasta_fn, outfile, \
lastz_bin, extra, mask, format, grid))
if grid:
cmds = [lastz_2bit(x) for x in args]
g = Grid(cmds)
g.run()
g.writestatus()
p = Pool(cpus)
p.map(lastz_2bit, args)
return
lock = Lock()
if grid:
cmds = [lastz(k + 1, cpus, bfasta_fn, afasta_fn, out_fh, \
lock, lastz_bin, extra, mask, grid) for k in xrange(cpus)]
mkdir(outdir)
g = Grid(cmds, outfiles=[op.join(outdir, "out.{0}.lastz").\
format(i) for i in range(len(cmds))])
g.run()
g.writestatus()
else:
args = [(k + 1, cpus, bfasta_fn, afasta_fn, out_fh, lock, lastz_bin,
extra, mask) for k in xrange(cpus)]
g = Jobs(target=lastz, args=args)
g.run()
def main(args):
"""
%prog database.fasta query.fasta
Run LAST by calling LASTDB, LASTAL and LASTEX.
"""
supported_formats = ("tab", "maf", "blast")
p = OptionParser(main.__doc__)
p.add_option("-a", "-A", dest="cpus", default=1, type="int",
help="parallelize job to multiple cpus [default: %default]")
p.add_option("--path", help="specify LAST path")
p.add_option("--format", default="blast", choices=supported_formats,
help="Output format, one of {0} [default: %default]".\
format("|".join(supported_formats)))
p.add_option("--eval", default=False, action="store_true",
help="Use lastex to recalculate E-value [default: %default]")
set_params(p)
set_outfile(p)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
subject, query = args
if opts.eval and opts.cpus > 1:
raise Exception, "Option --eval cannnot work with multiple threads"
path = opts.path
getpath = lambda x: op.join(path, x) if path else x
lastdb_bin = getpath("lastdb")
lastal_bin = getpath("lastal")
lastex_bin = getpath("lastex")
subjectdb = subject.rsplit(".", 1)[0]
run_lastdb(infile=subject, outfile=subjectdb + ".prj", lastdb_bin=lastdb_bin)
cpus = opts.cpus
logging.debug("Dispatch job to {0} cpus".format(cpus))
if opts.format == "maf":
cmd = 'echo "##maf version=1"'
sh(cmd)
cmd = "{0} -u 0".format(lastal_bin)
f = supported_formats.index(opts.format)
cmd += " -f {0}".format(f)
cmd += " {0} -".format(subjectdb)
extra = opts.extra
if extra:
cmd += " " + extra
if opts.eval:
querydb = query.rsplit(".", 1)[0]
run_lastdb(infile=query, outfile=querydb + ".prj")
cmd += " | {0} {1}.prj {2}.prj -".format(lastex_bin, subjectdb, querydb)
out_fh = must_open(opts.outfile, "w")
lock = Lock()
args = [(k + 1, cpus, out_fh, cmd, query, lock) \
for k in xrange(cpus)]
g = Jobs(target=last, args=args)
g.run()