def align(args):
"""
%prog align database.fasta read1.fq read2.fq
Wrapper for `gsnap` single-end or paired-end, depending on the number of
args.
"""
from jcvi.formats.fasta import join
from jcvi.formats.fastq import guessoffset
from jcvi.projects.tgbs import snp
p = OptionParser(align.__doc__)
p.add_option("--join", default=False, action="store_true",
help="Join sequences with padded 50Ns")
p.add_option("--rnaseq", default=False, action="store_true",
help="Input is RNA-seq reads, turn splicing on")
p.add_option("--snp", default=False, action="store_true",
help="Call SNPs after GSNAP")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) == 2:
logging.debug("Single-end alignment")
elif len(args) == 3:
logging.debug("Paired-end alignment")
else:
sys.exit(not p.print_help())
dbfile, readfile = args[0:2]
if opts.join:
dbfile = join([dbfile, "--gapsize=50", "--newid=chr1"])
assert op.exists(dbfile) and op.exists(readfile)
prefix = get_prefix(readfile, dbfile)
logfile = prefix + ".log"
gsnapfile = prefix + ".gsnap"
if not need_update((dbfile, readfile), gsnapfile):
logging.error("`{0}` exists. `gsnap` already run.".format(gsnapfile))
else:
dbdir, dbname = check_index(dbfile)
cmd = "gsnap -D {0} -d {1}".format(dbdir, dbname)
cmd += " -B 5 -m 0.1 -i 2 -n 3" # memory, mismatch, indel penalty, nhits
if opts.rnaseq:
cmd += " -N 1"
cmd += " -t {0}".format(opts.cpus)
cmd += " --gmap-mode none --nofails"
if readfile.endswith(".gz"):
cmd += " --gunzip"
try:
offset = "sanger" if guessoffset([readfile]) == 33 else "illumina"
cmd += " --quality-protocol {0}".format(offset)
except AssertionError:
pass
cmd += " " + " ".join(args[1:])
sh(cmd, outfile=gsnapfile, errfile=logfile)
if opts.snp:
snp([gsnapfile, "--cpus={0}".format(opts.cpus)])
return gsnapfile, logfile
def assemble(args):
"""
%prog assemble sffdir
Assemble each BAC separately using newbler.
"""
from jcvi.formats.fasta import join
p = OptionParser(assemble.__doc__)
p.add_option("--overwrite", default=False, action="store_true",
help="Overwrite the separate BAC assembly [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
sffdir, = args
asmdir = "newbler"
fastadir = "fasta"
mkdir(asmdir, overwrite=opts.overwrite)
mkdir(fastadir, overwrite=opts.overwrite)
cmd = "runAssembly -cpu 8 -o {0} {1}"
for sffile in glob("{0}/*.sff".format(sffdir)):
pf = op.basename(sffile).split(".")[1]
pf = pf.lower()
outdir = op.join(asmdir, pf)
if op.exists(outdir):
logging.debug("`{0}` exists. Ignored.".format(outdir))
continue
acmd = cmd.format(outdir, sffile)
sh(acmd)
ctgfile = op.join(outdir, "454LargeContigs.fna")
if not op.exists(ctgfile): # newbler failure
logging.error("File `{0}` not found (newbler failure).".\
format(ctgfile))
continue
outfile = op.join(fastadir, "{0}.fasta".format(pf))
newidopt = "--newid={0}".format(pf)
minctgsizeopt = "--minctgsize=200"
join([ctgfile, outfile, newidopt, minctgsizeopt])
def scaffold(args):
"""
%prog scaffold ctgfasta reads1.fasta mapping1.bed
reads2.fasta mapping2.bed ...
Run BAMBUS on set of contigs, reads and read mappings.
"""
from jcvi.formats.base import FileMerger
from jcvi.formats.bed import mates
from jcvi.formats.contig import frombed
from jcvi.formats.fasta import join
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.add_option("--conf",
help="BAMBUS configuration file [default: %default]")
p.add_option(
"--prefix",
default=False,
action="store_true",
help="Only keep links between IDs with same prefix [default: %default]"
)
opts, args = p.parse_args(args)
nargs = len(args)
if nargs < 3 or nargs % 2 != 1:
sys.exit(not p.print_help())
ctgfasta = args[0]
duos = list(grouper(2, args[1:]))
trios = []
for fastafile, bedfile in duos:
prefix = bedfile.rsplit(".", 1)[0]
matefile = prefix + ".mates"
matebedfile = matefile + ".bed"
if need_update(bedfile, [matefile, matebedfile]):
matesopt = [bedfile, "--lib", "--nointra"]
if opts.prefix:
matesopt += ["--prefix"]
matefile, matebedfile = mates(matesopt)
trios.append((fastafile, matebedfile, matefile))
# Merge the readfasta, bedfile and matefile
bbfasta, bbbed, bbmate = "bambus.reads.fasta", "bambus.bed", "bambus.mates"
for files, outfile in zip(zip(*trios), (bbfasta, bbbed, bbmate)):
FileMerger(files, outfile=outfile).merge(checkexists=True)
ctgfile = "bambus.contig"
idsfile = "bambus.ids"
frombedInputs = [bbbed, ctgfasta, bbfasta]
if need_update(frombedInputs, ctgfile):
frombed(frombedInputs)
inputfasta = "bambus.contigs.fasta"
singletonfasta = "bambus.singletons.fasta"
cmd = "faSomeRecords {0} {1} ".format(ctgfasta, idsfile)
sh(cmd + inputfasta)
sh(cmd + singletonfasta + " -exclude")
# Run bambus
prefix = "bambus"
cmd = "goBambus -c {0} -m {1} -o {2}".format(ctgfile, bbmate, prefix)
if opts.conf:
cmd += " -C {0}".format(opts.conf)
sh(cmd)
cmd = "untangle -e {0}.evidence.xml -s {0}.out.xml -o {0}.untangle.xml".\
format(prefix)
sh(cmd)
final = "final"
cmd = "printScaff -e {0}.evidence.xml -s {0}.untangle.xml -l {0}.lib " \
"-merge -detail -oo -sum -o {1}".format(prefix, final)
sh(cmd)
oofile = final + ".oo"
join([inputfasta, "--oo={0}".format(oofile)])
def align(args):
"""
%prog align database.fasta read1.fq read2.fq
Wrapper for `gsnap` single-end or paired-end, depending on the number of
args.
"""
from jcvi.formats.fasta import join
from jcvi.formats.fastq import guessoffset
from jcvi.projects.tgbs import snp
p = OptionParser(align.__doc__)
p.add_option("--join",
default=False,
action="store_true",
help="Join sequences with padded 50Ns")
p.add_option("--rnaseq",
default=False,
action="store_true",
help="Input is RNA-seq reads, turn splicing on")
p.add_option("--snp",
default=False,
action="store_true",
help="Call SNPs after GSNAP")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) == 2:
logging.debug("Single-end alignment")
elif len(args) == 3:
logging.debug("Paired-end alignment")
else:
sys.exit(not p.print_help())
dbfile, readfile = args[0:2]
if opts.join:
dbfile = join([dbfile, "--gapsize=50", "--newid=chr1"])
assert op.exists(dbfile) and op.exists(readfile)
prefix = get_prefix(readfile, dbfile)
logfile = prefix + ".log"
gsnapfile = prefix + ".gsnap"
if not need_update((dbfile, readfile), gsnapfile):
logging.error("`{0}` exists. `gsnap` already run.".format(gsnapfile))
else:
dbdir, dbname = check_index(dbfile)
cmd = "gsnap -D {0} -d {1}".format(dbdir, dbname)
cmd += " -B 5 -m 0.1 -i 2 -n 3" # memory, mismatch, indel penalty, nhits
if opts.rnaseq:
cmd += " -N 1"
cmd += " -t {0}".format(opts.cpus)
cmd += " --gmap-mode none --nofails"
if readfile.endswith(".gz"):
cmd += " --gunzip"
try:
offset = "sanger" if guessoffset([readfile]) == 33 else "illumina"
cmd += " --quality-protocol {0}".format(offset)
except AssertionError:
pass
cmd += " " + " ".join(args[1:])
sh(cmd, outfile=gsnapfile, errfile=logfile)
if opts.snp:
snp([gsnapfile, "--cpus={0}".format(opts.cpus)])
return gsnapfile, logfile
def scaffold(args):
"""
%prog scaffold ctgfasta reads1.fasta mapping1.bed
reads2.fasta mapping2.bed ...
Run BAMBUS on set of contigs, reads and read mappings.
"""
from jcvi.formats.base import FileMerger
from jcvi.formats.bed import mates
from jcvi.formats.contig import frombed
from jcvi.formats.fasta import join
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.set_rclip(rclip=1)
p.add_option("--conf", help="BAMBUS configuration file [default: %default]")
p.add_option("--prefix", default=False, action="store_true",
help="Only keep links between IDs with same prefix [default: %default]")
opts, args = p.parse_args(args)
nargs = len(args)
if nargs < 3 or nargs % 2 != 1:
sys.exit(not p.print_help())
rclip = opts.rclip
ctgfasta = args[0]
duos = list(grouper(args[1:], 2))
trios = []
for fastafile, bedfile in duos:
prefix = bedfile.rsplit(".", 1)[0]
matefile = prefix + ".mates"
matebedfile = matefile + ".bed"
if need_update(bedfile, [matefile, matebedfile]):
matesopt = [bedfile, "--lib", "--nointra",
"--rclip={0}".format(rclip),
"--cutoff={0}".format(opts.cutoff)]
if opts.prefix:
matesopt += ["--prefix"]
matefile, matebedfile = mates(matesopt)
trios.append((fastafile, matebedfile, matefile))
# Merge the readfasta, bedfile and matefile
bbfasta, bbbed, bbmate = "bambus.reads.fasta", "bambus.bed", "bambus.mates"
for files, outfile in zip(zip(*trios), (bbfasta, bbbed, bbmate)):
FileMerger(files, outfile=outfile).merge(checkexists=True)
ctgfile = "bambus.contig"
idsfile = "bambus.ids"
frombedInputs = [bbbed, ctgfasta, bbfasta]
if need_update(frombedInputs, ctgfile):
frombed(frombedInputs)
inputfasta = "bambus.contigs.fasta"
singletonfasta = "bambus.singletons.fasta"
cmd = "faSomeRecords {0} {1} ".format(ctgfasta, idsfile)
sh(cmd + inputfasta)
sh(cmd + singletonfasta + " -exclude")
# Run bambus
prefix = "bambus"
cmd = "goBambus -c {0} -m {1} -o {2}".format(ctgfile, bbmate, prefix)
if opts.conf:
cmd += " -C {0}".format(opts.conf)
sh(cmd)
cmd = "untangle -e {0}.evidence.xml -s {0}.out.xml -o {0}.untangle.xml".\
format(prefix)
sh(cmd)
final = "final"
cmd = "printScaff -e {0}.evidence.xml -s {0}.untangle.xml -l {0}.lib " \
"-merge -detail -oo -sum -o {1}".format(prefix, final)
sh(cmd)
oofile = final + ".oo"
join([inputfasta, "--oo={0}".format(oofile)])
