def main():
parser = build_construct_args()
parser.add_argument(
"--build-tagset", "-t", default=True, action="store_false", help="Construct tagset while loading sequences"
)
parser.add_argument("input_contigs")
parser.add_argument("input_reads", nargs="+")
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >> sys.stderr, "** WARNING: hashsize is default! You absodefly want to increase this!\n** Please read the docs!"
print >> sys.stderr, "\nPARAMETERS:"
print >> sys.stderr, " - kmer size = %d \t\t(-k)" % args.ksize
print >> sys.stderr, " - n hashes = %d \t\t(-N)" % args.n_hashes
print >> sys.stderr, " - min hashsize = %-5.2g \t(-x)" % args.min_hashsize
print >> sys.stderr, ""
print >> sys.stderr, "Estimated memory usage is %.2g bytes (n_hashes x min_hashsize / 8)" % (
args.n_hashes * args.min_hashsize / 8.0
)
print >> sys.stderr, "-" * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.input_contigs
filenames = args.input_reads
###
print "making hashtable"
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for filename in filenames:
print "consuming input", filename
ht.consume_fasta(filename)
###
print "reading contigs from", args.input_contigs
fp = open(os.path.basename(args.input_contigs) + ".unfound", "w")
for contig in screed.open(base):
seq = contig.sequence
n_not_found = 0
found = True
for start in range(0, len(seq) - K):
kmer = seq[start : start + K]
if not ht.get(kmer):
n_not_found += 1
found = False
if not found:
fp.write(">%s %d %d\n%s\n" % (contig.name, n_not_found, len(contig.sequence), contig.sequence))
def main():
parser = build_construct_args()
parser.add_argument("input_filenames", nargs="+")
parser.add_argument("read_filename")
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >> sys.stderr, "** WARNING: hashsize is default! " "You absodefly want to increase this!\n** " "Please read the docs!"
print >> sys.stderr, "\nPARAMETERS:"
print >> sys.stderr, " - kmer size = %d \t\t(-k)" % args.ksize
print >> sys.stderr, " - n hashes = %d \t\t(-N)" % args.n_hashes
print >> sys.stderr, " - min hashsize = %-5.2g \t(-x)" % args.min_hashsize
print >> sys.stderr, ""
print >> sys.stderr, "Estimated memory usage is %.2g bytes " "(n_hashes x min_hashsize / 8)" % (
args.n_hashes * args.min_hashsize * len(args.input_filenames) / 8.0
)
print >> sys.stderr, "-" * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inputlist = args.input_filenames
readsfile = args.read_filename
query_list = []
for n, inp_name in enumerate(inputlist):
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
outfile = os.path.basename(inp_name) + ".sweep3"
outfp = open(outfile, "w")
query_list.append((ht, outfp))
for n, inp_name in enumerate(inputlist):
ht = query_list[n][0]
# load contigs, connect into N partitions
print "loading input reads from", inp_name
ht.consume_fasta(inp_name)
print "starting sweep."
n = 0
m = 0
for n, record in enumerate(screed.open(readsfile)):
if len(record.sequence) < K:
continue
if n % 10000 == 0:
print "...", n, m
for ht, outfp in query_list:
count = ht.get_median_count(record.sequence)[0]
if count:
outfp.write(output_single(record))
def main():
parser = build_construct_args()
parser.add_argument('input_filename')
parser.add_argument('read_filename')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inp = args.input_filename
readsfile = args.read_filename
outfile = os.path.basename(readsfile) + '.sweep2'
outfp = open(outfile, 'w')
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# load contigs, connect into N partitions
print 'loading input reads from', inp
ht.consume_fasta(inp)
print 'starting sweep.'
n = 0
m = 0
for record in screed.open(readsfile):
if len(record.sequence) < K:
continue
if n % 10000 == 0:
print '...', n, m
count = ht.get_median_count(record.sequence)[0]
if count:
m += 1
outfp.write('>%s\n%s\n' % (record.name, record.sequence))
n += 1
def main():
parser = build_construct_args()
parser.add_argument('input_filename')
parser.add_argument('read_filename')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inp = args.input_filename
readsfile = args.read_filename
outfile = os.path.basename(readsfile) + '.sweep2'
outfp = open(outfile, 'w')
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# load contigs, connect into N partitions
print 'loading input reads from', inp
ht.consume_fasta(inp)
print 'starting sweep.'
n = 0
m = 0
for record in screed.open(readsfile):
if len(record.sequence) < K:
continue
if n % 10000 == 0:
print '...', n, m
count = ht.get_median_count(record.sequence)[0]
if count:
m += 1
outfp.write('>%s\n%s\n' % (record.name, record.sequence))
n += 1
def main():
parser = build_construct_args()
parser.add_argument('--build-tagset',
'-t',
default=True,
action='store_false',
help='Construct tagset while loading sequences')
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >> sys.stderr, "** WARNING: hashsize is default! You absodefly want to increase this!\n** Please read the docs!"
print >> sys.stderr, '\nPARAMETERS:'
print >> sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >> sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >> sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
print >> sys.stderr, ''
print >> sys.stderr, 'Estimated memory usage is %.2g bytes (n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >> sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.output_filename
filenames = args.input_filenames
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
###
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, filename in enumerate(filenames):
print 'consuming input', filename
ht.consume_fasta_and_tag(filename)
print 'saving hashtable in', base + '.ht'
ht.save(base + '.ht')
print 'saving tagset in', base + '.tagset'
ht.save_tagset(base + '.tagset')
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >> sys.stderr, "**"
print >> sys.stderr, "** ERROR: the graph structure is too small for"
print >> sys.stderr, "** this data set. Increase hashsize/num ht."
print >> sys.stderr, "**"
sys.exit(-1)
def main():
parser = build_construct_args()
parser.add_argument("input_filename")
parser.add_argument("read_filename")
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >> sys.stderr, "** WARNING: hashsize is default! " "You absodefly want to increase this!\n** " "Please read the docs!"
print >> sys.stderr, "\nPARAMETERS:"
print >> sys.stderr, " - kmer size = %d \t\t(-k)" % args.ksize
print >> sys.stderr, " - n hashes = %d \t\t(-N)" % args.n_hashes
print >> sys.stderr, " - min hashsize = %-5.2g \t(-x)" % args.min_hashsize
print >> sys.stderr, ""
print >> sys.stderr, "Estimated memory usage is %.2g bytes " "(n_hashes x min_hashsize / 8)" % (
args.n_hashes * args.min_hashsize / 8.0
)
print >> sys.stderr, "-" * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inp = args.input_filename
readsfile = args.read_filename
outfile = os.path.basename(readsfile) + ".sweep2"
outfp = open(outfile, "w")
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# load contigs, connect into N partitions
print "loading input reads from", inp
ht.consume_fasta(inp)
print "starting sweep."
n = 0
m = 0
for record in screed.open(readsfile):
if len(record.sequence) < K:
continue
if n % 10000 == 0:
print "...", n, m
count = ht.get_median_count(record.sequence)[0]
if count:
m += 1
outfp.write(">%s\n%s\n" % (record.name, record.sequence))
n += 1
def main():
parser = build_construct_args()
parser.add_argument('--build-tagset', '-t', default=True,
action='store_false',
help='Construct tagset while loading sequences')
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print>>sys.stderr, "** WARNING: hashsize is default! You absodefly want to increase this!\n** Please read the docs!"
print>>sys.stderr, '\nPARAMETERS:'
print>>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print>>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print>>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
print>>sys.stderr, ''
print>>sys.stderr, 'Estimated memory usage is %.2g bytes (n_hashes x min_hashsize / 8)' % (args.n_hashes * args.min_hashsize / 8.)
print>>sys.stderr, '-'*8
K=args.ksize
HT_SIZE=args.min_hashsize
N_HT=args.n_hashes
base = args.output_filename
filenames = args.input_filenames
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
###
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, filename in enumerate(filenames):
print 'consuming input', filename
ht.consume_fasta_and_tag(filename)
print 'saving hashtable in', base + '.ht'
ht.save(base + '.ht')
print 'saving tagset in', base + '.tagset'
ht.save_tagset(base + '.tagset')
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the graph structure is too small for"
print >>sys.stderr, "** this data set. Increase hashsize/num ht."
print >>sys.stderr, "**"
sys.exit(-1)
def main():
parser = build_construct_args()
parser.add_argument('input_filename')
parser.add_argument('read_filename')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inp = args.input_filename
readsfile = args.read_filename
tag = args.tag
outfile = os.path.basename(readsfile) + '.' + tag + '.sweep2'
outfp = open(outfile, 'w')
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# load contigs, connect into N partitions
print 'loading input reads from', inp
ht.consume_fasta(inp)
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.20:
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the counting hash is too small for"
print >>sys.stderr, "** this data set. Increase hashsize/num ht."
print >>sys.stderr, "**"
print >>sys.stderr, "** Do not use these results!!"
sys.exit(-1)
print 'starting sweep.'
n = 0
m = 0
for record in screed.open(readsfile):
if len(record.sequence) < K:
continue
if n % 100000 == 0:
print '...', n, m
count = ht.get_median_count(record.sequence)[0]
if count:
m += 1
outfp.write('>%s\n%s\n' % (record.name, record.sequence))
n += 1
def main():
parser = build_construct_args()
parser.add_argument('--subset-size', '-s', default=DEFAULT_SUBSET_SIZE,
dest='subset_size', type=float,
help='Set subset size (usually 1e5-1e6 is good)')
parser.add_argument('--no-big-traverse', dest='no_big_traverse',
action='store_true', default=False,
help='Truncate graph joins at big traversals')
parser.add_argument('--threads', '-T', dest='n_threads',
default=DEFAULT_N_THREADS,
help='Number of simultaneous threads to execute')
parser.add_argument('--keep-subsets', dest='remove_subsets',
default=True, action='store_false',
help='Keep individual subsets (default: False)')
parser.add_argument('graphbase')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, \
"** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, \
' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, \
'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' \
% (args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.graphbase
filenames = args.input_filenames
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
print '--'
print 'SUBSET SIZE', args.subset_size
print 'N THREADS', args.n_threads
print '--'
### load-graph
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, filename in enumerate(filenames):
print 'consuming input', filename
ht.consume_fasta_and_tag(filename)
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the graph structure is too small for"
print >>sys.stderr, "** this data set. Increase hashsize/num ht."
print >>sys.stderr, "**"
sys.exit(-1)
### partition-graph
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print '** This script brakes for lumps: stop_big_traversals is true.'
else:
print '** Traverse all the things: stop_big_traversals is false.'
#
# now, partition!
#
# divide the tags up into subsets
divvy = ht.divide_tags_into_subsets(int(args.subset_size))
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for i in range(0, n_subsets):
start = divvy[i]
end = divvy[i + 1]
worker_q.put((ht, i, start, end))
print 'enqueued %d subset tasks' % n_subsets
open('%s.info' % base, 'w').write('%d subsets total\n' % (n_subsets))
n_threads = int(args.n_threads)
if n_subsets < n_threads:
n_threads = n_subsets
# start threads!
print 'starting %d threads' % n_threads
print '---'
threads = []
for n in range(n_threads):
t = threading.Thread(target=worker, args=(worker_q, base,
stop_big_traversals))
threads.append(t)
t.start()
print 'done starting threads'
# wait for threads
for t in threads:
t.join()
print '---'
print 'done making subsets! see %s.subset.*.pmap' % (base,)
### merge-partitions
output_file = args.graphbase + '.pmap.merged'
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print 'loading %d pmap files (first one: %s)' % (len(pmap_files),
pmap_files[0])
ht = khmer.new_hashbits(K, 1, 1)
for pmap_file in pmap_files:
print 'merging', pmap_file
ht.merge_subset_from_disk(pmap_file)
if args.remove_subsets:
print 'removing pmap files'
for pmap_file in pmap_files:
os.unlink(pmap_file)
### annotate-partitions
for infile in args.input_filenames:
print 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
n = ht.output_partitions(infile, outfile)
print 'output %d partitions for %s' % (n, infile)
print 'partitions are in', outfile
def main():
parser = build_construct_args()
parser.add_argument('input_filenames', nargs='+')
parser.add_argument('read_filename')
parser.add_argument('tag')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize * len(args.input_filenames) / 8.)
print >>sys.stderr, '-'*8
K=args.ksize
HT_SIZE=args.min_hashsize
N_HT=args.n_hashes
inputlist = args.input_filenames
readsfile = args.read_filename
tag = args.tag
logfile = open('%s.sweep3.log' %(tag), 'wb')
query_list = []
for n, inp_name in enumerate(inputlist):
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
outfile = os.path.basename(inp_name) + '.' + tag + '.sweep3'
outfp = open(outfile, 'w')
query_list.append((ht, outfp))
new_lis = []
cnt = 0
for n, inp_name in enumerate(inputlist):
ht = query_list[n][0]
outfp = query_list[n][1]
# load contigs, connect into N partitions
print 'loading input reads from', inp_name
ht.consume_fasta(inp_name)
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.20:
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the counting hash is too small for"
print >>sys.stderr, "** %s. Increase hashsize/num ht." %(inp_name)
print >>sys.stderr, "**"
print >>sys.stderr, "** Do not use these results!!"
print >>sys.stderr, "%s is not processed, inscrease mem" %(inp_name)
print >> logfile, "%s is not processed, inscrease mem" %(inp_name)
cnt += 1
outfp.close()
os.remove('%s.sweep3' %os.path.basename(inp_name))
else:
new_lis.append(query_list[n])
print '%d files do not have enough mem assigned' %cnt
print 'starting sweep.'
n = 0
m = 0
for n, record in enumerate(screed.open(readsfile)):
if len(record.sequence) < K:
continue
if n % 100000 == 0:
print '...', n, m
for ht, outfp in new_lis:
count = ht.get_median_count(record.sequence)[0]
if count:
outfp.write('>%s\n%s\n' % (record.name, record.sequence))
def main():
parser = build_construct_args()
parser.add_argument('--build-tagset',
'-t',
default=True,
action='store_false',
help='Construct tagset while loading sequences')
parser.add_argument('input_contigs')
parser.add_argument('input_reads', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >> sys.stderr, '\nPARAMETERS:'
print >> sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >> sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >> sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >> sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.input_contigs
filenames = args.input_reads
###
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for filename in filenames:
print 'consuming input', filename
ht.consume_fasta(filename)
###
print 'reading contigs from', args.input_contigs
fp = open(os.path.basename(args.input_contigs) + '.unfound', 'w')
for contig in screed.open(base):
seq = contig.sequence
n_not_found = 0
found = True
for start in range(0, len(seq) - K):
kmer = seq[start:start + K]
if not ht.get(kmer):
n_not_found += 1
found = False
if not found:
fp.write('>%s %d %d\n%s\n' %
(contig.name, n_not_found, len(
contig.sequence), contig.sequence))
def main():
parser = build_construct_args()
parser.add_argument('--build-tagset', '-t', default=True,
action='store_false',
help='Construct tagset while loading sequences')
parser.add_argument('input_contigs')
parser.add_argument('input_reads', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.input_contigs
filenames = args.input_reads
###
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for filename in filenames:
print 'consuming input', filename
ht.consume_fasta(filename)
###
print 'reading contigs from', args.input_contigs
fp = open(os.path.basename(args.input_contigs) + '.unfound', 'w')
for contig in screed.open(base):
seq = contig.sequence
n_not_found = 0
found = True
for start in range(0, len(seq) - K):
kmer = seq[start:start + K]
if not ht.get(kmer):
n_not_found += 1
found = False
if not found:
fp.write('>%s %d %d\n%s\n' % (contig.name,
n_not_found, len(contig.sequence), contig.sequence))
def main():
parser = build_construct_args()
add_threading_args(parser)
parser.add_argument('--no-build-tagset', '-n', default=False,
action='store_true', dest='no_build_tagset',
help='Do NOT construct tagset while loading sequences')
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.output_filename
filenames = args.input_filenames
n_threads = int(args.n_threads)
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
if args.no_build_tagset:
print 'We WILL NOT build the tagset.'
else:
print 'We WILL build the tagset (for partitioning/traversal).'
#
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
if args.no_build_tagset:
target_method = ht.consume_fasta_with_reads_parser
else:
target_method = ht.consume_fasta_and_tag_with_reads_parser
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
for n, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input', filename
for tnum in xrange(n_threads):
t = threading.Thread(target=target_method, args=(rparser, ))
threads.append(t)
t.start()
for t in threads:
t.join()
print 'saving hashtable in', base + '.ht'
ht.save(base + '.ht')
if not args.no_build_tagset:
print 'saving tagset in', base + '.tagset'
ht.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % ht.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the graph structure is too small for"
print >>sys.stderr, "** this data set. Increase hashsize/num ht."
print >>sys.stderr, "**"
sys.exit(-1)
def main():
parser = build_construct_args()
parser.add_argument('input_filenames', nargs='+')
parser.add_argument('read_filename')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >> sys.stderr, '\nPARAMETERS:'
print >> sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >> sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
args.min_hashsize
print >> sys.stderr, ''
print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
args.n_hashes * args.min_hashsize * len(args.input_filenames) / 8.)
print >> sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
inputlist = args.input_filenames
readsfile = args.read_filename
query_list = []
for n, inp_name in enumerate(inputlist):
# create a hashbits data structure
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
outfile = os.path.basename(inp_name) + '.sweep3'
outfp = open(outfile, 'w')
query_list.append((ht, outfp))
for n, inp_name in enumerate(inputlist):
ht = query_list[n][0]
# load contigs, connect into N partitions
print 'loading input reads from', inp_name
ht.consume_fasta(inp_name)
print 'starting sweep.'
n = 0
m = 0
for n, record in enumerate(screed.open(readsfile)):
if len(record.sequence) < K:
continue
if n % 10000 == 0:
print '...', n, m
for ht, outfp in query_list:
count = ht.get_median_count(record.sequence)[0]
if count:
outfp.write(output_single(record))
def main():
parser = build_construct_args()
add_threading_args(parser)
parser.add_argument('--no-build-tagset',
'-n',
default=False,
action='store_true',
dest='no_build_tagset',
help='Do NOT construct tagset while loading sequences')
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.output_filename
filenames = args.input_filenames
n_threads = int(args.n_threads)
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
if args.no_build_tagset:
print 'We WILL NOT build the tagset.'
else:
print 'We WILL build the tagset (for partitioning/traversal).'
#
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
if args.no_build_tagset:
target_method = ht.consume_fasta_with_reads_parser
else:
target_method = ht.consume_fasta_and_tag_with_reads_parser
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
for n, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input', filename
for tnum in xrange(n_threads):
t = threading.Thread(target=target_method, args=(rparser, ))
threads.append(t)
t.start()
for t in threads:
t.join()
print 'saving hashtable in', base + '.ht'
ht.save(base + '.ht')
if not args.no_build_tagset:
print 'saving tagset in', base + '.tagset'
ht.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % ht.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >> sys.stderr, "**"
print >> sys.stderr, "** ERROR: the graph structure is too small for"
print >> sys.stderr, "** this data set. Increase hashsize/num ht."
print >> sys.stderr, "**"
sys.exit(-1)
def main():
parser = build_construct_args()
parser.add_argument('--subset-size', '-s', default=DEFAULT_SUBSET_SIZE,
dest='subset_size', type=float,
help='Set subset size (usually 1e5-1e6 is good)')
parser.add_argument('--no-big-traverse', dest='no_big_traverse',
action='store_true', default=False,
help='Truncate graph joins at big traversals')
parser.add_argument('--threads', '-T', dest='n_threads',
default=DEFAULT_N_THREADS,
help='Number of simultaneous threads to execute')
parser.add_argument('--keep-subsets', dest='remove_subsets',
default=True, action='store_false',
help='Keep individual subsets (default: False)')
parser.add_argument('graphbase')
parser.add_argument('input_filenames', nargs='+')
args = parser.parse_args()
if not args.quiet:
if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
print >>sys.stderr, \
"** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
"Please read the docs!"
print >>sys.stderr, '\nPARAMETERS:'
print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
print >>sys.stderr, \
' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
print >>sys.stderr, ''
print >>sys.stderr, \
'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' \
% (args.n_hashes * args.min_hashsize / 8.)
print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
base = args.graphbase
filenames = args.input_filenames
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
print '--'
print 'SUBSET SIZE', args.subset_size
print 'N THREADS', args.n_threads
print '--'
# load-graph
print 'making hashtable'
ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, filename in enumerate(filenames):
print 'consuming input', filename
ht.consume_fasta_and_tag(filename)
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, "**"
print >>sys.stderr, "** ERROR: the graph structure is too small for"
print >>sys.stderr, "** this data set. Increase hashsize/num ht."
print >>sys.stderr, "**"
sys.exit(-1)
# partition-graph
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print '** This script brakes for lumps: stop_big_traversals is true.'
else:
print '** Traverse all the things: stop_big_traversals is false.'
#
# now, partition!
#
# divide the tags up into subsets
divvy = ht.divide_tags_into_subsets(int(args.subset_size))
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for i in range(0, n_subsets):
start = divvy[i]
end = divvy[i + 1]
worker_q.put((ht, i, start, end))
print 'enqueued %d subset tasks' % n_subsets
open('%s.info' % base, 'w').write('%d subsets total\n' % (n_subsets))
n_threads = int(args.n_threads)
if n_subsets < n_threads:
n_threads = n_subsets
# start threads!
print 'starting %d threads' % n_threads
print '---'
threads = []
for n in range(n_threads):
t = threading.Thread(target=worker, args=(worker_q, base,
stop_big_traversals))
threads.append(t)
t.start()
print 'done starting threads'
# wait for threads
for t in threads:
t.join()
print '---'
print 'done making subsets! see %s.subset.*.pmap' % (base,)
# merge-partitions
output_file = args.graphbase + '.pmap.merged'
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print 'loading %d pmap files (first one: %s)' % (len(pmap_files),
pmap_files[0])
ht = khmer.new_hashbits(K, 1, 1)
for pmap_file in pmap_files:
print 'merging', pmap_file
ht.merge_subset_from_disk(pmap_file)
if args.remove_subsets:
print 'removing pmap files'
for pmap_file in pmap_files:
os.unlink(pmap_file)
# annotate-partitions
for infile in args.input_filenames:
print 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
n = ht.output_partitions(infile, outfile)
print 'output %d partitions for %s' % (n, infile)
print 'partitions are in', outfile