def count(args):
"""
%prog count fastafile jf.db
Run dump - jellyfish - bin - bincount in serial.
"""
from bitarray import bitarray
p = OptionParser(count.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, jfdb = args
K = get_K(jfdb)
cmd = "jellyfish query {0} -C | cut -d' ' -f 2".format(jfdb)
t = must_open("tmp", "w")
proc = Popen(cmd, stdin=PIPE, stdout=t)
t.flush()
f = Fasta(fastafile, lazy=True)
for name, rec in f.iteritems_ordered():
kmers = list(make_kmers(rec.seq, K))
print("\n".join(kmers), file=proc.stdin)
proc.stdin.close()
logging.debug(cmd)
proc.wait()
a = bitarray()
binfile = ".".join((fastafile, jfdb, "bin"))
fw = open(binfile, "w")
t.seek(0)
for row in t:
c = row.strip()
a.append(int(c))
a.tofile(fw)
logging.debug("Serialize {0} bits to `{1}`.".format(len(a), binfile))
fw.close()
sh("rm {0}".format(t.name))
logging.debug(
"Shared K-mers (K={0}) between `{1}` and `{2}` written to `{3}`.".format(
K, fastafile, jfdb, binfile
)
)
cntfile = ".".join((fastafile, jfdb, "cnt"))
bincount([fastafile, binfile, "-o", cntfile, "-K {0}".format(K)])
logging.debug("Shared K-mer counts written to `{0}`.".format(cntfile))
def append(args):
"""
%prog append bamfile
Append /1 or /2 to read names. Useful for using the Tophat2 bam file for
training AUGUSTUS gene models.
"""
p = OptionParser(append.__doc__)
p.add_option("--prepend", help="Prepend string to read names")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(bamfile,) = args
prepend = opts.prepend
icmd = "samtools view -h {0}".format(bamfile)
bamfile = bamfile.rsplit(".", 1)[0] + ".append.bam"
ocmd = "samtools view -b -@ 64 - -o {0}".format(bamfile)
p = Popen(ocmd, stdin=PIPE)
for row in popen(icmd):
if row[0] == "@":
print(row.strip(), file=p.stdin)
else:
s = SamLine(row)
if prepend:
s.qname = prepend + "_" + s.qname
else:
s.update_readname()
print(s, file=p.stdin)
def append(args):
"""
%prog append bamfile
Append /1 or /2 to read names. Useful for using the Tophat2 bam file for
training AUGUSTUS gene models.
"""
p = OptionParser(append.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bamfile, = args
icmd = "samtools view -h {0}".format(bamfile)
bamfile = bamfile.rsplit(".", 1)[0] + ".append.bam"
ocmd = "samtools view -b -@ 64 - -o {0}".format(bamfile)
p = Popen(ocmd, stdin=PIPE)
for row in popen(icmd):
if row[0] == '@':
print >> p.stdin, row.strip()
else:
s = SamLine(row)
s.update_readname()
print >> p.stdin, s
def lastz_2bit(t):
"""
Used for formats other than BLAST, i.e. lav, maf, etc. which requires the
database file to contain a single FASTA record.
"""
bfasta_fn, afasta_fn, outfile, lastz_bin, extra, mask, format = t
ref_tags = [Darkspace]
qry_tags = [Darkspace]
ref_tags, qry_tags = add_mask(ref_tags, qry_tags, mask=mask)
lastz_cmd = Lastz_template.format(lastz_bin, bfasta_fn, ref_tags, \
afasta_fn, qry_tags)
if extra:
lastz_cmd += " " + extra.strip()
lastz_cmd += " --format={0}".format(format)
proc = Popen(lastz_cmd)
out_fh = open(outfile, "w")
logging.debug("job <%d> started: %s" % (proc.pid, lastz_cmd))
for row in proc.stdout:
out_fh.write(row)
out_fh.flush()
logging.debug("job <%d> finished" % proc.pid)
def lastz(k, n, bfasta_fn, afasta_fn, out_fh, lock, lastz_bin, extra,
mask=False):
ref_tags = [Multiple, Darkspace]
qry_tags = [Darkspace]
if n != 1:
qry_tags.append(Subsample.format(k, n))
ref_tags, qry_tags = add_mask(ref_tags, qry_tags, mask=mask)
lastz_cmd = Lastz_template.format(lastz_bin, bfasta_fn, ref_tags, \
afasta_fn, qry_tags)
if extra:
lastz_cmd += " " + extra.strip()
lastz_cmd += " --format=general-:%s" % lastz_fields
# The above conversion is no longer necessary after LASTZ v1.02.40
# (of which I contributed a patch)
#lastz_cmd += " --format=BLASTN-"
proc = Popen(lastz_cmd)
logging.debug("job <%d> started: %s" % (proc.pid, lastz_cmd))
for row in proc.stdout:
row = lastz_to_blast(row)
lock.acquire()
print >> out_fh, row
out_fh.flush()
lock.release()
logging.debug("job <%d> finished" % proc.pid)
def count(args):
"""
%prog count fastafile jf.db
Run dump - jellyfish - bin - bincount in serial.
"""
from bitarray import bitarray
p = OptionParser(count.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, jfdb = args
K = get_K(jfdb)
cmd = "jellyfish query {0} -C | cut -d' ' -f 2".format(jfdb)
t = must_open("tmp", "w")
proc = Popen(cmd, stdin=PIPE, stdout=t)
t.flush()
f = Fasta(fastafile, lazy=True)
for name, rec in f.iteritems_ordered():
kmers = list(make_kmers(rec.seq, K))
print >> proc.stdin, "\n".join(kmers)
proc.stdin.close()
logging.debug(cmd)
proc.wait()
a = bitarray()
binfile = ".".join((fastafile, jfdb, "bin"))
fw = open(binfile, "w")
t.seek(0)
for row in t:
c = row.strip()
a.append(int(c))
a.tofile(fw)
logging.debug("Serialize {0} bits to `{1}`.".format(len(a), binfile))
fw.close()
sh("rm {0}".format(t.name))
logging.debug("Shared K-mers (K={0}) between `{1}` and `{2}` written to `{3}`.".\
format(K, fastafile, jfdb, binfile))
cntfile = ".".join((fastafile, jfdb, "cnt"))
bincount([fastafile, binfile, "-o", cntfile, "-K {0}".format(K)])
logging.debug("Shared K-mer counts written to `{0}`.".format(cntfile))
def blastplus(out_fh, cmd, query, lock):
cmd += " -query {0}".format(query)
proc = Popen(cmd)
logging.debug("job <%d> started: %s" % (proc.pid, cmd))
for row in proc.stdout:
if row[0] == '#':
continue
lock.acquire()
out_fh.write(row)
out_fh.flush()
lock.release()
logging.debug("job <%d> finished" % proc.pid)
def last(k, n, out_fh, cmd, query, lock):
proc = Popen(cmd, stdin=PIPE)
parser = SeqIO.parse(query, "fasta")
for rec in islice(parser, k - 1, None, n):
SeqIO.write([rec], proc.stdin, "fasta")
proc.stdin.close()
logging.debug("job <%d> started: %s" % (proc.pid, cmd))
for row in proc.stdout:
if row[0] == '#':
continue
lock.acquire()
out_fh.write(row)
out_fh.flush()
lock.release()
logging.debug("job <%d> finished" % proc.pid)
def run(self):
r = Popen(str(self))
return r.communicate()
def run(self):
r = Popen(str(self))
return r.communicate()
