def blast(args):
"""
%prog blast ref.fasta query.fasta
Calls blast and then filter the BLAST hits. Default is megablast.
"""
from jcvi.apps.command import run_megablast
task_choices = ("blastn", "blastn-short", "dc-megablast", \
"megablast", "vecscreen")
p = OptionParser(blast.__doc__)
p.add_option("--best", default=1, type="int",
help="Only look for best N hits [default: %default]")
p.add_option("--task", default="megablast", choices=task_choices,
help="Task of the blastn, one of {0}".\
format("|".join(task_choices)) + " [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
reffasta, queryfasta = args
q = op.basename(queryfasta).split(".")[0]
r = op.basename(reffasta).split(".")[0]
blastfile = "{0}.{1}.blast".format(q, r)
run_megablast(infile=queryfasta, outfile=blastfile, db=reffasta, \
pctid=None, hitlen=None, best=opts.best, task=opts.task)
def blast(args):
"""
%prog blast allfasta clonename
Insert a component into agpfile by aligning to the best hit in pool and see
if they have good overlaps.
"""
from jcvi.apps.command import run_megablast
p = OptionParser(blast.__doc__)
p.add_option("-n",
type="int",
default=2,
help="Take best N hits [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
allfasta, clonename = args
fastadir = "fasta"
infile = op.join(fastadir, clonename + ".fasta")
if not op.exists(infile):
fetch([clonename, "--skipcheck", "--outdir=" + fastadir])
outfile = "{0}.{1}.blast".format(clonename, allfasta.split(".")[0])
run_megablast(infile=infile, outfile=outfile, db=allfasta, \
pctid=GoodPct, hitlen=GoodOverlap)
blasts = [BlastLine(x) for x in open(outfile)]
besthits = []
for b in blasts:
if b.query.count("|") >= 3:
b.query = b.query.split("|")[3]
if b.subject.count("|") >= 3:
b.subject = b.subject.split("|")[3]
b.query = b.query.rsplit(".", 1)[0]
b.subject = b.subject.rsplit(".", 1)[0]
if b.query == b.subject:
continue
if b.subject not in besthits:
besthits.append(b.subject)
if len(besthits) == opts.n:
break
for b in besthits:
overlap([clonename, b, "--dir=" + fastadir])
def blast(args):
"""
%prog blast allfasta clonename
Insert a component into agpfile by aligning to the best hit in pool and see
if they have good overlaps.
"""
from jcvi.apps.command import run_megablast
p = OptionParser(blast.__doc__)
p.add_option("-n", type="int", default=2,
help="Take best N hits [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
allfasta, clonename = args
fastadir = "fasta"
infile = op.join(fastadir, clonename + ".fasta")
if not op.exists(infile):
fetch([clonename, "--skipcheck", "--outdir=" + fastadir])
outfile = "{0}.{1}.blast".format(clonename, allfasta.split(".")[0])
run_megablast(infile=infile, outfile=outfile, db=allfasta, \
pctid=GoodPct, hitlen=GoodOverlap)
blasts = [BlastLine(x) for x in open(outfile)]
besthits = []
for b in blasts:
if b.query.count("|") >= 3:
b.query = b.query.split("|")[3]
if b.subject.count("|") >= 3:
b.subject = b.subject.split("|")[3]
b.query = b.query.rsplit(".", 1)[0]
b.subject = b.subject.rsplit(".", 1)[0]
if b.query == b.subject:
continue
if b.subject not in besthits:
besthits.append(b.subject)
if len(besthits) == opts.n:
break
for b in besthits:
overlap([clonename, b, "--dir=" + fastadir])
def blast(args):
"""
%prog blast ref.fasta query.fasta
Calls blast and then filter the BLAST hits. Default is megablast.
"""
from jcvi.apps.command import run_megablast
task_choices = ("blastn", "blastn-short", "dc-megablast", \
"megablast", "vecscreen")
p = OptionParser(blast.__doc__)
p.add_option("--pctid",
type="int",
help="Percent identity [default: %default]")
p.add_option("--wordsize",
type="int",
help="Word size [default: %default]")
p.add_option("--best",
default=1,
type="int",
help="Only look for best N hits [default: %default]")
p.add_option("--task", default="megablast", choices=task_choices,
help="Task of the blastn, one of {0}".\
format("|".join(task_choices)) + " [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
reffasta, queryfasta = args
q = op.basename(queryfasta).split(".")[0]
r = op.basename(reffasta).split(".")[0]
blastfile = "{0}.{1}.blast".format(q, r)
run_megablast(infile=queryfasta, outfile=blastfile, db=reffasta, \
wordsize=opts.wordsize, pctid=opts.pctid,
hitlen=None, best=opts.best, task=opts.task)
return blastfile
def overlap(args):
"""
%prog overlap ctgfasta poolfasta
Fish out the sequences in `poolfasta` that overlap with `ctgfasta`.
Mix and combine using `minimus2`.
"""
p = OptionParser(overlap.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, poolfasta = args
prefix = ctgfasta.split(".")[0]
rid = list(Fasta(ctgfasta).iterkeys())
assert len(rid) == 1, "Use overlapbatch() to improve multi-FASTA file"
rid = rid[0]
splitctgfasta = ctgfasta.rsplit(".", 1)[0] + ".split.fasta"
ctgfasta = run_gapsplit(infile=ctgfasta, outfile=splitctgfasta)
# Run BLAST
blastfile = ctgfasta + ".blast"
run_megablast(infile=ctgfasta, outfile=blastfile, db=poolfasta)
# Extract contigs and merge using minimus2
closuredir = prefix + ".closure"
closure = False
if need_update(blastfile, closuredir):
mkdir(closuredir, overwrite=True)
closure = True
if closure:
idsfile = op.join(closuredir, prefix + ".ids")
cmd = "cut -f2 {0} | sort -u".format(blastfile)
sh(cmd, outfile=idsfile)
idsfastafile = op.join(closuredir, prefix + ".ids.fasta")
cmd = "faSomeRecords {0} {1} {2}".format(poolfasta, idsfile, idsfastafile)
sh(cmd)
# This step is a hack to weight the bases from original sequences more
# than the pulled sequences, by literally adding another copy to be used
# in consensus calls.
redundantfastafile = op.join(closuredir, prefix + ".redundant.fasta")
format([ctgfasta, redundantfastafile, "--prefix=RED."])
mergedfastafile = op.join(closuredir, prefix + ".merged.fasta")
cmd = "cat {0} {1} {2}".format(ctgfasta, redundantfastafile, idsfastafile)
sh(cmd, outfile=mergedfastafile)
afgfile = op.join(closuredir, prefix + ".afg")
cmd = "toAmos -s {0} -o {1}".format(mergedfastafile, afgfile)
sh(cmd)
cwd = os.getcwd()
os.chdir(closuredir)
cmd = "minimus2 {0} -D REFCOUNT=0".format(prefix)
cmd += " -D OVERLAP=100 -D MINID=98"
sh(cmd)
os.chdir(cwd)
# Analyze output, make sure that:
# + Get the singletons of the original set back
# + Drop any contig that is comprised entirely of pulled set
originalIDs = set(Fasta(ctgfasta).iterkeys())
minimuscontig = op.join(closuredir, prefix + ".contig")
c = ContigFile(minimuscontig)
excludecontigs = set()
for rec in c.iter_records():
reads = set(x.id for x in rec.reads)
if reads.isdisjoint(originalIDs):
excludecontigs.add(rec.id)
logging.debug("Exclude contigs: {0}".\
format(", ".join(sorted(excludecontigs))))
finalfasta = prefix + ".improved.fasta_"
fw = open(finalfasta, "w")
minimusfasta = op.join(closuredir, prefix + ".fasta")
f = Fasta(minimusfasta)
for id, rec in f.iteritems_ordered():
if id in excludecontigs:
continue
SeqIO.write([rec], fw, "fasta")
singletonfile = op.join(closuredir, prefix + ".singletons")
singletons = set(x.strip() for x in open(singletonfile))
leftovers = singletons & originalIDs
logging.debug("Pull leftover singletons: {0}".\
format(", ".join(sorted(leftovers))))
f = Fasta(ctgfasta)
for id, rec in f.iteritems_ordered():
if id not in leftovers:
continue
SeqIO.write([rec], fw, "fasta")
fw.close()
fastafile = finalfasta
finalfasta = fastafile.rstrip("_")
format([fastafile, finalfasta, "--sequential", "--pad0=3",
"--prefix={0}_".format(rid)])
logging.debug("Improved FASTA written to `{0}`.".format(finalfasta))
n50([ctgfasta])
n50([finalfasta])
errlog = "error.log"
for f in (fastafile, blastfile, errlog):
if op.exists(f):
os.remove(f)
