def get_parser():
epilog = """
Note: with :option:`-b` the output will be the exact size of the
k-mer counting table and this script will use a constant amount of memory.
In exchange k-mer counts will stop at 255. The memory usage of this script
with :option:`-b` will be about 1.15x the product of the :option:`-x` and
:option:`-N` numbers.
Example::
load_into_counting.py -k 20 -x 5e7 out.kh data/100k-filtered.fa
Multiple threads can be used to accelerate the process, if you have extra
cores to spare.
Example::
load_into_counting.py -k 20 -x 5e7 -T 4 out.kh data/100k-filtered.fa
"""
parser = build_counting_args("Build a k-mer counting table from the given"
" sequences.", epilog=textwrap.dedent(epilog))
add_threading_args(parser)
parser.add_argument('output_countingtable_filename', help="The name of the"
" file to write the k-mer counting table to.")
parser.add_argument('input_sequence_filename', nargs='+',
help="The names of one or more FAST[AQ] input "
"sequence files.")
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
return parser
def get_parser():
parser = build_hashbits_args(descr="Load sequences into the compressible "
"graph format plus optional tagset.")
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',
metavar='output_presence_table_filename',
help='output'
' k-mer presence table filename.')
parser.add_argument('input_filenames',
metavar='input_sequence_filename',
nargs='+',
help='input FAST[AQ] sequence filename')
parser.add_argument('--report-total-kmers',
'-t',
action='store_true',
help="Prints the total number of k-mers to stderr")
parser.add_argument('--write-fp-rate',
'-w',
action='store_true',
help="Write false positive rate into .info file")
return parser
def get_parser():
epilog = """
Note: with :option:`-b` the output will be the exact size of the
k-mer counting table and this script will use a constant amount of memory.
In exchange k-mer counts will stop at 255. The memory usage of this script
with :option:`-b` will be about 1.15x the product of the :option:`-x` and
:option:`-N` numbers.
Example::
load-into-counting.py -k 20 -x 5e7 out.kh data/100k-filtered.fa
Multiple threads can be used to accelerate the process, if you have extra
cores to spare.
Example::
load_into_counting.py -k 20 -x 5e7 -T 4 out.kh data/100k-filtered.fa
"""
parser = build_counting_args("Build a k-mer counting table from the given"
" sequences.", epilog=textwrap.dedent(epilog))
add_threading_args(parser)
parser.add_argument('output_countingtable_filename', help="The name of the"
" file to write the k-mer counting table to.")
parser.add_argument('input_sequence_filename', nargs='+',
help="The names of one or more FAST[AQ] input "
"sequence files.")
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
parser.add_argument('--report-total-kmers', '-t', action='store_true',
help="Prints the total number of k-mers to stderr")
return parser
def main():
parser = build_construct_args()
add_threading_args(parser)
parser.add_argument('datafile')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
filename = args.datafile
### first, load reads into hash table
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input, round 1 --', filename
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
### now, count.
total = 0
total_unique = 0
for n, record in enumerate(screed.open(filename)):
total += 1
last_kmer = record.sequence[-K:]
count = ht.get(last_kmer)
if count == 1:
total_unique += 1
print 'singletons: %d unique; of %d total; %.3f' % \
(total_unique, total, total_unique/float(total))
def main():
parser = build_construct_args()
add_threading_args(parser)
parser.add_argument('datafile')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
filename = args.datafile
### first, load reads into hash table
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input, round 1 --', filename
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
### now, count.
total = 0
total_unique = 0
for n, record in enumerate(screed.open(filename)):
total += 1
last_kmer = record.sequence[-K:]
count = ht.get(last_kmer)
if count == 1:
total_unique += 1
print 'singletons: %d unique; of %d total; %.3f' % \
(total_unique, total, total_unique/float(total))
def get_parser():
parser = build_hashbits_args(descr="Load sequences into the compressible "
"graph format plus optional tagset.")
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',
metavar='output_presence_table_filename', help='output'
' k-mer presence table filename.')
parser.add_argument('input_filenames', metavar='input_sequence_filename',
nargs='+', help='input FAST[AQ] sequence filename')
return parser
def get_parser():
parser = build_hashbits_args(descr="Load sequences into the compressible "
"graph format plus optional tagset.")
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',
metavar='output_presence_table_filename', help='output'
' k-mer presence table filename.')
parser.add_argument('input_filenames', metavar='input_sequence_filename',
nargs='+', help='input FAST[AQ] sequence filename')
parser.add_argument('--report-total-kmers', '-t', action='store_true',
help="Prints the total number of k-mers to stderr")
parser.add_argument('--write-fp-rate', '-w', action='store_true',
help="Write false positive rate into .info file")
return parser
def get_parser():
parser = build_hashbits_args(descr="Load sequences into the compressible "
"graph format plus optional tagset.")
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',
metavar='output_presence_table_filename',
help='output'
' k-mer presence table filename.')
parser.add_argument('input_filenames',
metavar='input_sequence_filename',
nargs='+',
help='input FAST[AQ] sequence filename')
return parser
def main():
parser = build_construct_args()
add_threading_args(parser)
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
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)
###
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
ht.set_use_bigcount(args.bigcount)
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=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
if n > 0 and n % 10 == 0:
print 'mid-save', base
ht.save(base)
open(base + '.info', 'w').write('through %s' % filename)
print 'saving', base
ht.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filename)
# 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
print >>info_fp, '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, "**"
sys.exit(-1)
print 'DONE.'
def main():
parser = build_construct_args(
"Output k-mer abundance distribution (single file version).")
add_threading_args(parser)
parser.add_argument('datafile')
parser.add_argument('histout')
parser.add_argument('-z', '--no-zero', dest='output_zero', default=True,
action='store_false',
help='Do not output 0-count bins')
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
parser.add_argument('-s', '--squash', dest='squash_output', default=False,
action='store_true',
help='Overwrite output file if it exists')
parser.add_argument('--savehash', dest='savehash', default='')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
datafile = args.datafile
histout = args.histout
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
ht.set_use_bigcount(args.bigcount)
print 'building tracking ht'
K = ht.ksize()
sizes = ht.hashsizes()
tracking = khmer._new_hashbits(K, sizes)
print 'K:', K
print 'HT sizes:', sizes
print 'outputting to', histout
config = khmer.get_config()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
# start loading
rparser = khmer.ReadParser(datafile, n_threads)
threads = []
print 'consuming input, round 1 --', datafile
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
z_list = []
def do_abundance_dist(r):
z = ht.abundance_distribution_with_reads_parser(r, tracking)
z_list.append(z)
print 'preparing hist from %s...' % datafile
rparser = khmer.ReadParser(datafile, n_threads)
threads = []
print 'consuming input, round 2 --', datafile
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=do_abundance_dist,
args=(rparser,)
)
threads.append(t)
t.start()
for t in threads:
t.join()
assert len(z_list) == n_threads, len(z_list)
z = {}
for zz in z_list:
for i, count in enumerate(zz):
z[i] = z.get(i, 0) + count
total = sum(z.values())
if 0 == total:
print >>sys.stderr, \
"ERROR: abundance distribution is uniformly zero; " \
"nothing to report."
print >>sys.stderr, "\tPlease verify that the input files are valid."
sys.exit(-1)
fp = open(histout, 'w')
sofar = 0
for n, i in sorted(z.items()):
if i == 0 and not args.output_zero:
continue
sofar += i
frac = sofar / float(total)
print >>fp, n, i, sofar, round(frac, 3)
if sofar == total:
break
if args.savehash:
print 'Saving hashfile', args.savehash
print '...saving to', args.savehash
ht.save(args.savehash)
def main():
parser = build_construct_args()
add_threading_args(parser)
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)' \
% (args.n_hashes * args.min_hashsize)
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
n_threads = int(args.n_threads)
print 'Saving hashtable to %s' % base
print 'Loading kmers from sequences in %s' % repr(filenames)
###
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
ht.set_use_bigcount(True)
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=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
# ht.consume_fasta(filename)
for t in threads:
t.join()
if n > 0 and n % 10 == 0:
print 'mid-save', base
ht.save(base)
open(base + '.info', 'w').write('through %s' % filename)
print 'saving', base
ht.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filename)
# 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
print >>info_fp, '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, "**"
sys.exit(-1)
print 'DONE.'
def main():
parser = build_construct_args(
"Output k-mer abundance distribution (single file version).")
add_threading_args(parser)
parser.add_argument('datafile')
parser.add_argument('histout')
parser.add_argument('-z',
'--no-zero',
dest='output_zero',
default=True,
action='store_false',
help='Do not output 0-count bins')
parser.add_argument('-b',
'--no-bigcount',
dest='bigcount',
default=True,
action='store_false',
help='Do not count k-mers past 255')
parser.add_argument('-s',
'--squash',
dest='squash_output',
default=False,
action='store_true',
help='Overwrite output file if it exists')
parser.add_argument('--savehash', dest='savehash', default='')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
datafile = args.datafile
histout = args.histout
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
ht.set_use_bigcount(args.bigcount)
print 'building tracking ht'
K = ht.ksize()
sizes = ht.hashsizes()
tracking = khmer._new_hashbits(K, sizes)
print 'K:', K
print 'HT sizes:', sizes
print 'outputting to', histout
config = khmer.get_config()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
# start loading
rparser = khmer.ReadParser(datafile, n_threads)
threads = []
print 'consuming input, round 1 --', datafile
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
z_list = []
def do_abundance_dist(r):
z = ht.abundance_distribution_with_reads_parser(r, tracking)
z_list.append(z)
print 'preparing hist from %s...' % datafile
rparser = khmer.ReadParser(datafile, n_threads)
threads = []
print 'consuming input, round 2 --', datafile
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=do_abundance_dist,
args=(rparser,)
)
threads.append(t)
t.start()
for t in threads:
t.join()
assert len(z_list) == n_threads, len(z_list)
z = {}
for zz in z_list:
for i, count in enumerate(zz):
z[i] = z.get(i, 0) + count
total = sum(z.values())
if 0 == total:
print >>sys.stderr, \
"ERROR: abundance distribution is uniformly zero; " \
"nothing to report."
print >> sys.stderr, "\tPlease verify that the input files are valid."
sys.exit(-1)
fp = open(histout, 'w')
sofar = 0
for n, i in sorted(z.items()):
if i == 0 and not args.output_zero:
continue
sofar += i
frac = sofar / float(total)
print >> fp, n, i, sofar, round(frac, 3)
if sofar == total:
break
if args.savehash:
print 'Saving hashfile', args.savehash
print '...saving to', args.savehash
ht.save(args.savehash)
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()
add_threading_args(parser)
parser.add_argument('output_filename')
parser.add_argument('input_filenames', nargs='+')
parser.add_argument('-b',
'--no-bigcount',
dest='bigcount',
default=True,
action='store_false',
help='Do not count k-mers past 255')
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)
#
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
ht.set_use_bigcount(args.bigcount)
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=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
if n > 0 and n % 10 == 0:
print 'mid-save', base
ht.save(base)
open(base + '.info', 'w').write('through %s' % filename)
print 'saving', base
ht.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filename)
# 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
print >> info_fp, '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, "**"
sys.exit(-1)
print 'DONE.'
def main():
parser = build_construct_args(
"Filter k-mers at the given abundance (inmem version).")
add_threading_args(parser)
parser.add_argument('--cutoff',
'-C',
dest='cutoff',
default=DEFAULT_CUTOFF,
type=int,
help="Trim at k-mers below this abundance.")
parser.add_argument('--savehash', dest='savehash', default='')
parser.add_argument('datafile')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
filename = args.datafile
# first, load reads into hash table
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input, round 1 --', filename
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
# now, trim.
# the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
trim_seq, trim_at = ht.trim_on_abundance(seq, args.cutoff)
if trim_at >= K:
return name, trim_seq
return None, None
# the filtering loop
print 'filtering', filename
outfile = os.path.basename(filename) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(filename), outfp)
print 'output in', outfile
if args.savehash:
print 'Saving hashfile', args.savehash
print '...saving to', args.savehash
ht.save(args.savehash)
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(
"Filter k-mers at the given abundance (inmem version).")
add_threading_args(parser)
parser.add_argument('--cutoff', '-C', dest='cutoff',
default=DEFAULT_CUTOFF, type=int,
help="Trim at k-mers below this abundance.")
parser.add_argument('--savehash', dest='savehash', default='')
parser.add_argument('datafile')
args = parser.parse_args()
report_on_config(args)
K = args.ksize
HT_SIZE = args.min_hashsize
N_HT = args.n_hashes
n_threads = int(args.n_threads)
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
config.set_reads_input_buffer_size(n_threads * 64 * 1024)
print 'making hashtable'
ht = khmer.new_counting_hash(K, HT_SIZE, N_HT, n_threads)
filename = args.datafile
### first, load reads into hash table
rparser = khmer.ReadParser(filename, n_threads)
threads = []
print 'consuming input, round 1 --', filename
for tnum in xrange(n_threads):
t = \
threading.Thread(
target=ht.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(t)
t.start()
for t in threads:
t.join()
fp_rate = khmer.calc_expected_collisions(ht)
print 'fp rate estimated to be %1.3f' % fp_rate
### now, trim.
### the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
trim_seq, trim_at = ht.trim_on_abundance(seq, args.cutoff)
if trim_at >= K:
return name, trim_seq
return None, None
### the filtering loop
print 'filtering', filename
outfile = os.path.basename(filename) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(filename), outfp)
print 'output in', outfile
if args.savehash:
print 'Saving hashfile', args.savehash
print '...saving to', args.savehash
ht.save(args.savehash)
% scripts/count-median.py <htname> <input seqs> <output counts>
Use '-h' for parameter help.
The output is pickled dict contains sequence id, median.
NOTE: All 'N's in the input sequences are converted to 'G's.
"""
#def main():
start = time.time()
parser = argparse.ArgumentParser(
description='Count k-mers summary stats for sequences')
add_threading_args(parser)
parser.add_argument('htfile')
parser.add_argument('input')
parser.add_argument('output')
args = parser.parse_args()
htfile = args.htfile
input_filename = args.input
output_filename = args.output
n_threads = int(args.n_threads)
config = khmer.get_config()
bufsz = config.get_reads_input_buffer_size()
