def test_save_load(tabletype):
kh = tabletype(5, PRIMES_1m)
savefile = utils.get_temp_filename('tablesave.out')
# test add(dna)
x = kh.add("ATGGC")
z = kh.get("ATGGC")
assert z == 1
kh.save(savefile)
# should we provide a single load function here? yes, probably. @CTB
if tabletype == _Countgraph:
loaded = khmer.load_countgraph(savefile)
elif tabletype == _Counttable:
loaded = khmer.load_counttable(savefile)
elif tabletype == _SmallCountgraph:
loaded = khmer.load_countgraph(savefile, small=True)
elif tabletype == _SmallCounttable:
loaded = khmer.load_counttable(savefile, small=True)
elif tabletype == _Nodegraph:
loaded = khmer.load_nodegraph(savefile)
elif tabletype == _Nodetable:
loaded = khmer.load_nodetable(savefile)
else:
raise Exception("unknown tabletype")
z = loaded.get('ATGGC')
assert z == 1
def test_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave1.ht')
loadpath = utils.get_temp_filename('tempcountingsave1.ht.gz')
sizes = list(PRIMES_1m)
sizes.append(1000005)
# save uncompressed hashtable.
hi = khmer._Countgraph(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
# compress.
in_file = open(savepath, 'rb')
out_file = gzip.open(loadpath, 'wb')
out_file.writelines(in_file)
out_file.close()
in_file.close()
# load compressed hashtable.
try:
ht = khmer.load_countgraph(loadpath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
tracking = khmer._Nodegraph(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
tracking = khmer._Nodegraph(12, sizes)
y = ht.abundance_distribution(inpath, tracking)
assert sum(x) == 3966, sum(x)
assert x == y, (x, y)
def main():
info("count-median.py", ["diginorm"])
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print("loading k-mer countgraph from", htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print("writing to", output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(["name", "median", "average", "stddev", "seqlen"])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if "N" in seq:
seq = seq.replace("N", "A")
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
def main():
counting_ht = sys.argv[1]
infiles = sys.argv[2:]
print('file with ht: %s' % counting_ht)
print('-- settings:')
print('N THREADS', WORKER_THREADS)
print('--')
print('making hashtable')
ht = khmer.load_countgraph(counting_ht)
K = ht.ksize()
for infile in infiles:
print('filtering', infile)
outfile = os.path.basename(infile) + '.below'
outfp = open(outfile, 'w')
def process_fn(record, ht=ht):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
if trim_at >= K:
return name, trim_seq
return None, None
tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
tsp.start(verbose_fasta_iter(infile), outfp)
def main():
hashfile = sys.argv[1]
filename = sys.argv[2]
figure = sys.argv[3]
ht = khmer.load_countgraph(hashfile)
outabund = open(os.path.basename(filename) + '.counts', 'w')
counts = []
d = {}
for sequence in open(sys.argv[2]):
sequence = sequence.strip()
count = ht.get(sequence)
counts.append(count)
d[count] = d.get(count, 0) + 1
if count > 1000:
print(sequence, count, file=outabund)
outfp = open(figure + '.countshist', 'w')
sofar = 0
sofar_cumu = 0
for k in sorted(d.keys()):
sofar += d[k]
sofar_cumu += k * d[k]
print(k, d[k], sofar, sofar_cumu, file=outfp)
hist(counts, normed=True, cumulative=True, bins=100, range=(1, 1000))
savefig(figure)
def test_load_into_counting_1():
in1 = utils.get_test_data("test-abund-read-2.fa")
out1 = utils.get_temp_filename("out.ct")
cmd = """
cat {in1} |
{scripts}/load-into-counting.py -x 1e3 -N 2 -k 20 {out1} - \
2> /dev/null
"""
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
print(cmd)
(status, out, err) = run_shell_cmd(cmd)
assert os.path.exists(out1)
khmer.load_countgraph(out1)
def test_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave1.ht')
loadpath = utils.get_temp_filename('tempcountingsave1.ht.gz')
sizes = list(PRIMES_1m)
sizes.append(1000005)
# save uncompressed hashtable.
hi = khmer._Countgraph(12, sizes)
hi.consume_seqfile(inpath)
hi.save(savepath)
# compress.
in_file = open(savepath, 'rb')
out_file = gzip.open(loadpath, 'wb')
out_file.writelines(in_file)
out_file.close()
in_file.close()
# load compressed hashtable.
try:
ht = khmer.load_countgraph(loadpath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
tracking = khmer._Nodegraph(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
tracking = khmer._Nodegraph(12, sizes)
y = ht.abundance_distribution(inpath, tracking)
assert sum(x) == 3966, sum(x)
assert x == y, (x, y)
def test_abund_dist_gz_bigcount_compressed_first():
infile = utils.copy_test_data('test-abund-read-2.fa')
script = 'load-into-counting.py'
htfile = utils.get_temp_filename('test_ct.gz')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
utils.runscript(script, args) # create a bigcount table
assert os.path.exists(htfile)
data = gzip.open(htfile, 'rb').read() # read compressed bigcount table
outfile = utils.get_temp_filename('test_ct')
f_out = open(outfile, 'wb') # output the bigcount table
f_out.write(data)
f_out.close()
# load the compressed bigcount table
try:
countgraph = khmer.load_countgraph(outfile)
except OSError as err:
assert 0, 'Should not produce OSError: ' + str(err)
assert countgraph.n_occupied() != 0
hashsizes = countgraph.hashsizes()
kmer_size = countgraph.ksize()
tracking = khmer._Nodegraph(kmer_size, hashsizes)
abundances = countgraph.abundance_distribution(infile, tracking)
# calculate abundance distribution for compressed bigcount table
flag = False
# check if abundance is > 255
# if ok gzipped bigcount was loaded correctly
for _, i in enumerate(abundances):
print(_, i)
if _ > 255 and i > 0:
flag = True
break
assert flag
def test_badload():
try:
countgraph = khmer.load_countgraph()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
def main():
info('count-kmers.py', ['counting'])
args = get_parser().parse_args()
print('hashtable from', args.input_count_graph_filename, file=sys.stderr)
countgraph = khmer.load_countgraph(args.input_count_graph_filename)
kmer_size = countgraph.ksize()
hashsizes = countgraph.hashsizes()
tracking = khmer._Nodegraph( # pylint: disable=protected-access
kmer_size, hashsizes)
if args.output_file is None:
args.output_file = sys.stdout
writer = csv.writer(args.output_file)
for filename in args.input_sequence_filenames:
for record in screed.open(filename):
seq = record.sequence.replace('N', 'A')
for i in range(len(seq) - kmer_size + 1):
kmer = seq[i:i + kmer_size]
if not tracking.get(kmer):
tracking.count(kmer)
writer.writerow([kmer, str(countgraph.get(kmer))])
print('Total number of unique k-mers: {0}'.format(
countgraph.n_unique_kmers()),
file=sys.stderr)
def test_load_into_counting_1():
in1 = utils.get_test_data('test-abund-read-2.fa')
out1 = utils.get_temp_filename('out.ct')
cmd = """
cat {in1} |
{scripts}/load-into-counting.py -x 1e3 -N 2 -k 20 {out1} - \
2> /dev/null
"""
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
print(cmd)
run_shell_cmd(cmd)
assert os.path.exists(out1)
khmer.load_countgraph(out1)
def main():
counting_ht = sys.argv[1]
infiles = sys.argv[2:]
print('file with ht: %s' % counting_ht)
print('-- settings:')
print('N THREADS', WORKER_THREADS)
print('--')
print('making hashtable')
ht = khmer.load_countgraph(counting_ht)
K = ht.ksize()
for infile in infiles:
print('filtering', infile)
outfile = os.path.basename(infile) + '.below'
outfp = open(outfile, 'w')
def process_fn(record, ht=ht):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
trim_seq, trim_at = ht.trim_below_abundance(seq, CUTOFF)
if trim_at >= K:
return name, trim_seq
return None, None
tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
tsp.start(verbose_fasta_iter(infile), outfp)
def main():
info('count-kmers.py', ['counting'])
args = get_parser().parse_args()
print ('hashtable from', args.input_count_graph_filename,
file=sys.stderr)
countgraph = khmer.load_countgraph(
args.input_count_graph_filename)
kmer_size = countgraph.ksize()
hashsizes = countgraph.hashsizes()
tracking = khmer._Nodegraph( # pylint: disable=protected-access
kmer_size, hashsizes)
if args.output_file is None:
args.output_file = sys.stdout
writer = csv.writer(args.output_file)
for filename in args.input_sequence_filenames:
for record in screed.open(filename):
seq = record.sequence.replace('N', 'A')
for i in range(len(seq) - kmer_size + 1):
kmer = seq[i:i+kmer_size]
if not tracking.get(kmer):
tracking.count(kmer)
writer.writerow([kmer, str(countgraph.get(kmer))])
print ('Total number of unique k-mers: {0}'.format(
countgraph.n_unique_kmers()), file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print('loading k-mer countgraph from', htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print('writing to', output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(['name', 'median', 'average', 'stddev', 'seqlen'])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
def test_abund_dist_gz_bigcount_compressed_first():
infile = utils.copy_test_data('test-abund-read-2.fa')
script = 'load-into-counting.py'
htfile = utils.get_temp_filename('test_ct.gz')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
utils.runscript(script, args) # create a bigcount table
assert os.path.exists(htfile)
data = gzip.open(htfile, 'rb').read() # read compressed bigcount table
outfile = utils.get_temp_filename('test_ct')
f_out = open(outfile, 'wb') # output the bigcount table
f_out.write(data)
f_out.close()
# load the compressed bigcount table
try:
countgraph = khmer.load_countgraph(outfile)
except OSError as err:
assert 0, 'Should not produce OSError: ' + str(err)
assert countgraph.n_occupied() != 0
hashsizes = countgraph.hashsizes()
kmer_size = countgraph.ksize()
tracking = khmer._Nodegraph(kmer_size, hashsizes)
abundances = countgraph.abundance_distribution(infile, tracking)
# calculate abundance distribution for compressed bigcount table
flag = False
# check if abundance is > 255
# if ok gzipped bigcount was loaded correctly
for _, i in enumerate(abundances):
print(_, i)
if _ > 255 and i > 0:
flag = True
break
assert flag
def main():
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print('loading k-mer countgraph from', htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print('writing to', output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(['name', 'median', 'average', 'stddev', 'seqlen'])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
def main():
info('filter-abund.py', ['counting'])
args = sanitize_help(get_parser()).parse_args()
check_input_files(args.input_graph, args.force)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
print("Accepting input from stdin; output filename must "
"be provided with -o.", file=sys.stderr)
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
print('loading countgraph:', args.input_graph,
file=sys.stderr)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
print("K:", ksize, file=sys.stderr)
# the filtering function.
def process_fn(record):
name = record.name
seq = record.sequence
seqN = seq.replace('N', 'A')
if args.variable_coverage: # only trim when sequence has high enough C
med, _, _ = countgraph.get_median_count(seqN)
if med < args.normalize_to:
return name, seq
_, trim_at = countgraph.trim_on_abundance(seqN, args.cutoff)
if trim_at >= ksize:
# be sure to not to change the 'N's in the trimmed sequence -
# so, return 'seq' and not 'seqN'.
return name, seq[:trim_at]
return None, None
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
print('filtering', infile, file=sys.stderr)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
tsp.start(verbose_loader(infile), outfp)
print('output in', outfile, file=sys.stderr)
def test_badload():
try:
countgraph = khmer.load_countgraph()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
def test_counting_gz_file_type_check():
inpath = utils.get_test_data('goodversion-k12.ht.gz')
try:
kh = khmer.load_countgraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
def test_load_gz_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
def test_load_gz_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('tempnodegraphsave0.htable')
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError:
pass
def test_counting_gz_file_type_check():
inpath = utils.get_test_data('goodversion-k12.ht.gz')
try:
kh = khmer.load_countgraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('tempnodegraphsave0.htable')
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError:
pass
def main():
parser = build_counting_multifile_args()
parser.add_argument('--coverage',
'-C',
dest='coverage',
default=DEFAULT_COVERAGE,
type=int)
args = parser.parse_args()
counting_ht = args.input_table
infiles = args.input_filenames
print('file with ht: %s' % counting_ht)
print('loading hashtable')
ht = khmer.load_countgraph(counting_ht)
K = ht.ksize()
xxxfp = None
print("K:", K)
# the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
med, avg, dev = ht.get_median_count(seq)
pct = dev / avg * 100
xxxfp.write('%s %s %s %s %s\n' % (med, avg, dev, pct, name))
if random.randint(1, med) > args.coverage or pct > 100:
return None, None
return name, seq
# the filtering loop
for infile in infiles:
print('filtering', infile)
xxxfp = open(os.path.basename(infile) + '.medpctfilt.stats', 'w')
outfile = os.path.basename(infile) + '.medpctfilt'
outfp = open(outfile, 'w')
for n, record in enumerate(screed.open(infile)):
if n % 100000 == 0:
print('...', n)
name, seq = process_fn(record)
if name and seq:
print('>%s\n%s' % (name, seq), file=outfp)
print('output in', outfile)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-m', '--min-coverage', type=int, default=None)
parser.add_argument('-M', '--max-coverage', type=int, default=None)
parser.add_argument('input_count_graph')
parser.add_argument('input_readfile')
parser.add_argument('output_readfile')
args = parser.parse_args()
print('min_coverage: %s' % args.min_coverage, file=sys.stderr)
print('max_coverage: %s' % args.max_coverage, file=sys.stderr)
if not (args.min_coverage or args.max_coverage):
print("neither min nor max coverage specified!? exiting!",
file=sys.stderr)
sys.exit(1)
if args.min_coverage and args.max_coverage and \
args.max_coverage < args.min_coverage:
print("min_coverage > max_coverage!? exiting!", file=sys.stderr)
sys.exit(1)
htable = khmer.load_countgraph(args.input_count_graph)
output_file = args.output_readfile
output_fp = open(output_file, 'w')
n_kept = 0
n = 0
for n, record in enumerate(screed.open(args.input_readfile)):
if n % 100000 == 0:
print('...', n, n_kept, file=sys.stderr)
seq = record.sequence.upper()
seq = seq.replace('N', 'A')
try:
med, _, _ = htable.get_median_count(seq)
except ValueError:
continue
keep = True
if args.min_coverage and med < args.min_coverage:
keep = False
if args.max_coverage and med > args.max_coverage:
keep = False
if keep:
n_kept += 1
output_fp.write(output_single(record))
print('consumed %d reads; kept %d' % (n, n_kept), file=sys.stderr)
def main():
parser = khmer_args.build_counting_args(
"Correct reads against an already-computed table",
citations=['counting', 'SeqAn'])
parser.add_argument("--trusted-cov",
dest="trusted_cov",
type=int,
default=DEFAULT_CUTOFF)
parser.add_argument("--theta", dest="bits_theta", type=float, default=1.0)
parser.add_argument('-o',
'--output',
dest='output_file',
help="output file for histogram; defaults to "
"<first filename>.corr in cwd.",
type=khFileType('w'),
default=None)
parser.add_argument('counts_table')
parser.add_argument('readfile')
args = parser.parse_args()
print('loading counts')
ht = khmer.load_countgraph(args.counts_table)
aligner = khmer.ReadAligner(ht, args.trusted_cov, args.bits_theta)
print("trusted:", args.trusted_cov)
corrfp = args.output_file
if not corrfp:
outfile = os.path.basename(args.readfile) + '.corr'
corrfp = open(outfile, 'w')
n_corrected = 0
for n, read in enumerate(screed.open(args.readfile)):
if n % 10000 == 0:
print('...', n, n_corrected, file=sys.stderr)
seq = read.sequence.replace('N', 'A')
# build the alignment...
score, graph_alignment, read_alignment, truncated = \
aligner.align(seq)
if not truncated:
graph_seq = graph_alignment.replace("-", "")
if graph_seq != seq:
n_corrected += 1
seq = graph_seq
corrfp.write(output_single(read, seq))
def main():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund.py', ['counting'])
configure_logging(args.quiet)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
log_info('loading countgraph: {graph}', graph=args.input_graph)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
log_info("K: {ksize}", ksize=ksize)
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
log_info('filtering {infile}', infile=infile)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
paired_iter = broken_paired_reader(ReadParser(infile),
min_length=ksize,
force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
args.variable_coverage,
args.normalize_to)
if trimmed_record:
write_record(trimmed_record, outfp)
log_info('output in {outfile}', outfile=outfile)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-m', '--min-coverage', type=int, default=None)
parser.add_argument('-M', '--max-coverage', type=int, default=None)
parser.add_argument('input_count_graph')
parser.add_argument('input_readfile')
parser.add_argument('output_readfile')
args = parser.parse_args()
print('min_coverage: %s' % args.min_coverage, file=sys.stderr)
print('max_coverage: %s' % args.max_coverage, file=sys.stderr)
if not (args.min_coverage or args.max_coverage):
print("neither min nor max coverage specified!? exiting!", file=sys.stderr)
sys.exit(1)
if args.min_coverage and args.max_coverage and \
args.max_coverage < args.min_coverage:
print("min_coverage > max_coverage!? exiting!", file=sys.stderr)
sys.exit(1)
htable = khmer.load_countgraph(args.input_count_graph)
output_file = args.output_readfile
output_fp = open(output_file, 'w')
n_kept = 0
n = 0
for n, record in enumerate(screed.open(args.input_readfile)):
if n % 100000 == 0:
print('...', n, n_kept, file=sys.stderr)
seq = record.sequence.upper()
seq = seq.replace('N', 'A')
try:
med, _, _ = htable.get_median_count(seq)
except ValueError:
continue
keep = True
if args.min_coverage and med < args.min_coverage:
keep = False
if args.max_coverage and med > args.max_coverage:
keep = False
if keep:
n_kept += 1
output_fp.write(output_single(record))
print('consumed %d reads; kept %d' % (n, n_kept), file=sys.stderr)
def main():
files = sys.argv[2:]
total_reads = len(files) * [0]
n_consumed = len(files) * [0]
n_seq_kept = len(files) * [0]
print('loading ht')
ht = khmer.load_countgraph(sys.argv[1])
for i, infile in enumerate(files):
print('outputting', infile + '.freq')
ht.output_fasta_kmer_pos_freq(infile, infile + ".freq")
def test_load_truncated():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('save.ht')
truncpath = utils.get_temp_filename('trunc.ht')
sizes = khmer.get_n_primes_near_x(3, 200)
hi = khmer._Countgraph(12, sizes)
hi.consume_seqfile(inpath)
hi.save(savepath)
data = open(savepath, 'rb').read()
for i in range(len(data)):
fp = open(truncpath, 'wb')
fp.write(data[:i])
fp.close()
try:
khmer.load_countgraph(truncpath)
assert 0, "this should not be reached!"
except OSError as err:
print(str(err))
def main():
args = get_parser().parse_args()
infiles = [args.input_count_graph_filename] + args.input_sequence_filenames
for infile in infiles:
check_input_files(infile, False)
counts = khmer.load_countgraph(args.input_count_graph_filename)
results = find_N_most_abundant_kmers(args.input_sequence_filenames,
args.N, counts)
results_df = pd.DataFrame({'kmer': [str(k) for k in results.keys()],
'count': [int(c) for c in results.values()]})
results_df.sort_values(by='count', inplace=True, ascending=False)
results_df.to_csv(args.output, index=False)
def test_load_truncated():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('save.ht')
truncpath = utils.get_temp_filename('trunc.ht')
sizes = khmer.get_n_primes_near_x(3, 200)
hi = khmer._Countgraph(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
data = open(savepath, 'rb').read()
for i in range(len(data)):
fp = open(truncpath, 'wb')
fp.write(data[:i])
fp.close()
try:
khmer.load_countgraph(truncpath)
assert 0, "this should not be reached!"
except OSError as err:
print(str(err))
def main():
parser = argparse.ArgumentParser()
parser.add_argument('table')
parser.add_argument('sequences')
parser.add_argument('-C', '--cutoff', default=3, type=int)
parser.add_argument('--coverage', default=20, type=int)
parser.add_argument('-V', '--variable', default=False, action='store_true')
parser.add_argument('-o', '--outfile', type=argparse.FileType('w'),
default=sys.stdout)
args = parser.parse_args()
kh = khmer.load_countgraph(args.table)
n_skipped_variable = 0
n_total = 0
print >>sys.stderr, "K:", kh.ksize()
print >>sys.stderr, "CUTOFF:", args.cutoff
if args.variable:
print >>sys.stderr, "variable coverage flag set;"
print >>sys.stderr, "NORMALIZE_LIMIT:", args.coverage
else:
print >>sys.stderr, "assuming even coverage - no -V"
for n, record in enumerate(screed.open(args.sequences)):
if n % 100000 == 0:
print >>sys.stderr, '...', n
seq = record.sequence.upper().replace('N', 'A')
n_total += 1
varskip = False
if args.variable:
med, _, _ = kh.get_median_count(seq)
if med < args.coverage:
varskip = True
n_skipped_variable += 1
name = record.name.split()[0]
if varskip:
print >>args.outfile, name, 'V'
else:
#posns = find_spectral_error_positions(kh, seq, args.cutoff)
posns = kh.find_spectral_error_positions(seq, args.cutoff)
posns = add_n_posns(posns, record.sequence)
print >>args.outfile, name, ",".join(map(str, posns))
if args.variable:
sys.stderr.write('Skipped %d reads of %d total due to -V\n' % \
(n_skipped_variable, n_total))
def main():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
log_info('loading countgraph: {graph}', graph=args.input_graph)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
log_info("K: {ksize}", ksize=ksize)
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
log_info('filtering {infile}', infile=infile)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
paired_iter = broken_paired_reader(ReadParser(infile),
min_length=ksize,
force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
args.variable_coverage,
args.normalize_to)
if trimmed_record:
write_record(trimmed_record, outfp)
log_info('output in {outfile}', outfile=outfile)
def main():
parser = build_counting_multifile_args()
parser.add_argument('--coverage', '-C', dest='coverage',
default=DEFAULT_COVERAGE, type=int)
args = parser.parse_args()
counting_ht = args.input_table
infiles = args.input_filenames
print('file with ht: %s' % counting_ht)
print('loading hashtable')
ht = khmer.load_countgraph(counting_ht)
K = ht.ksize()
xxxfp = None
print("K:", K)
# the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
med, avg, dev = ht.get_median_count(seq)
pct = dev / avg * 100
xxxfp.write('%s %s %s %s %s\n' % (med, avg, dev, pct, name))
if random.randint(1, med) > args.coverage or pct > 100:
return None, None
return name, seq
# the filtering loop
for infile in infiles:
print('filtering', infile)
xxxfp = open(os.path.basename(infile) + '.medpctfilt.stats', 'w')
outfile = os.path.basename(infile) + '.medpctfilt'
outfp = open(outfile, 'w')
for n, record in enumerate(screed.open(infile)):
if n % 100000 == 0:
print('...', n)
name, seq = process_fn(record)
if name and seq:
print('>%s\n%s' % (name, seq), file=outfp)
print('output in', outfile)
def main():
hashfile = sys.argv[1]
filename = sys.argv[2]
outfile = os.path.basename(filename)
print('loading kh file', hashfile)
ht = khmer.load_countgraph(hashfile)
x = ht.fasta_count_kmers_by_position(filename, 100, 1)
write_dist(x, open(outfile + '.pos.abund=1', 'w'))
print('wrote', outfile + '.pos.abund=1')
y = ht.fasta_count_kmers_by_position(filename, 100, 255)
write_dist(y, open(outfile + '.pos.abund=255', 'w'))
print('wrote', outfile + '.pos.abund=255')
def do_test(ctfile):
print('working with', ctfile)
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename(ctfile)
orig = khmer.Countgraph(12, 1e5, 4)
orig.consume_fasta(inpath)
orig.save(savepath)
loaded = khmer.load_countgraph(savepath)
orig_count = orig.n_occupied()
loaded_count = loaded.n_occupied()
assert orig_count == 3886, orig_count
assert loaded_count == orig_count, loaded_count
def test_save_load_occupied_small(ctfile):
print('working with', ctfile)
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename(ctfile)
orig = khmer.SmallCountgraph(12, 1e5, 4)
orig.consume_seqfile(inpath)
orig.save(savepath)
loaded = khmer.load_countgraph(savepath, small=True)
orig_count = orig.n_occupied()
loaded_count = loaded.n_occupied()
assert orig_count == 3886, orig_count
assert loaded_count == orig_count, loaded_count
def main():
parser = argparse.ArgumentParser(
description="Output k-mer abundance distribution.")
parser.add_argument('hashname')
parser.add_argument('seqfile')
parser.add_argument('histout')
args = parser.parse_args()
hashfile = args.hashname
seqfile = args.seqfile
histout = args.histout
outfp = open(histout, 'w')
print('hashtable from', hashfile)
ht = khmer.load_countgraph(hashfile)
hist = {}
for i in range(65536):
hist[i] = 0
for n, record in enumerate(screed.open(seqfile)):
if n > 0 and n % 100000 == 0:
print('...', n)
seq = record.sequence.replace('N', 'A')
try:
med, _, _ = ht.get_median_count(seq)
except ValueError:
continue
hist[med] = hist[med] + 1
histlist = list(hist.items())
histlist.sort()
maxk = max(hist.keys())
sumk = sum(hist.values())
sofar = 0
for n, m in histlist:
sofar += m
percent = float(sofar) / sumk
outfp.write('%d %d %d %.3f\n' % (n, m, sofar, percent))
outfp.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--trusted-cov", dest="trusted_cov", type=int,
default=DEFAULT_CUTOFF)
parser.add_argument("--theta", dest="bits_theta", type=float, default=1.0)
parser.add_argument('-o', '--output', dest='output_file',
help="output file for histogram; defaults to "
"<first filename>.errhist in cwd.",
type=argparse.FileType('w'), default=None)
parser.add_argument('counts_table')
parser.add_argument('readfile')
args = parser.parse_args()
print('loading counts')
ht = khmer.load_countgraph(args.counts_table)
aligner = khmer.ReadAligner(ht,
args.trusted_cov,
args.bits_theta)
print("trusted:", args.trusted_cov)
corrfp = args.output_file
if not corrfp:
outfile = os.path.basename(args.readfile) + '.corr'
corrfp = open(outfile, 'w')
n_corrected = 0
for n, read in enumerate(screed.open(args.readfile)):
if n % 10000 == 0:
print('...', n, n_corrected, file=sys.stderr)
seq = read.sequence.replace('N', 'A')
# build the alignment...
score, graph_alignment, read_alignment, truncated = \
aligner.align(seq)
if not truncated:
graph_seq = graph_alignment.replace("-", "")
if graph_seq != seq:
n_corrected += 1
seq = graph_seq
corrfp.write(output_single(read, seq))
def main():
parser = argparse.ArgumentParser(
description="Output k-mer abundance distribution.")
parser.add_argument('hashname')
parser.add_argument('seqfile')
parser.add_argument('histout')
args = parser.parse_args()
hashfile = args.hashname
seqfile = args.seqfile
histout = args.histout
outfp = open(histout, 'w')
print('hashtable from', hashfile)
ht = khmer.load_countgraph(hashfile)
hist = {}
for i in range(65536):
hist[i] = 0
for n, record in enumerate(screed.open(seqfile)):
if n > 0 and n % 100000 == 0:
print('...', n)
seq = record.sequence.replace('N', 'A')
try:
med, _, _ = ht.get_median_count(seq)
except ValueError:
continue
hist[med] = hist[med] + 1
histlist = list(hist.items())
histlist.sort()
maxk = max(hist.keys())
sumk = sum(hist.values())
sofar = 0
for n, m in histlist:
sofar += m
percent = float(sofar) / sumk
outfp.write('%d %d %d %.3f\n' % (n, m, sofar, percent))
outfp.close()
def test_save_load_large(ctfile):
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename(ctfile)
sizes = khmer.get_n_primes_near_x(1, 2**31 + 1000)
orig = khmer._Countgraph(12, sizes)
orig.consume_seqfile(inpath)
orig.save(savepath)
loaded = khmer.load_countgraph(savepath)
orig_count = orig.n_occupied()
loaded_count = loaded.n_occupied()
assert orig_count == 3966, orig_count
assert loaded_count == orig_count, loaded_count
def do_test(ctfile):
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename(ctfile)
sizes = khmer.get_n_primes_near_x(1, 2 ** 31 + 1000)
orig = khmer._Countgraph(12, sizes)
orig.consume_fasta(inpath)
orig.save(savepath)
loaded = khmer.load_countgraph(savepath)
orig_count = orig.n_occupied()
loaded_count = loaded.n_occupied()
assert orig_count == 3966, orig_count
assert loaded_count == orig_count, loaded_count
def test_normalize_by_median_no_bigcount():
infile = utils.copy_test_data('test-abund-read-2.fa')
hashfile = utils.get_temp_filename('test-out.ct')
in_dir = os.path.dirname(infile)
_make_counting(infile, K=8)
script = 'normalize-by-median.py'
args = ['-C', '1000', '-k 8', '--savegraph', hashfile, infile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0, (out, err)
print((out, err))
assert os.path.exists(hashfile), hashfile
kh = khmer.load_countgraph(hashfile)
assert kh.get('GGTTGACG') == 255
def test_normalize_by_median_no_bigcount():
infile = utils.get_temp_filename('test.fa')
hashfile = utils.get_temp_filename('test-out.ct')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
_make_counting(infile, K=8)
script = 'normalize-by-median.py'
args = ['-C', '1000', '-k 8', '--savegraph', hashfile, infile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0, (out, err)
print((out, err))
assert os.path.exists(hashfile), hashfile
kh = khmer.load_countgraph(hashfile)
assert kh.get('GGTTGACG') == 255
def main():
parser = build_counting_args()
parser.add_argument('--coverage',
'-C',
dest='coverage',
default=DEFAULT_COVERAGE,
type=int)
args = parser.parse_args()
counting_ht = args.input_table
infiles = args.input_filenames
print('file with ht: %s' % counting_ht)
print('loading hashtable')
ht = khmer.load_countgraph(counting_ht)
K = ht.ksize()
print("K:", K)
# the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
med, avg, dev = ht.get_median_count(seq)
if random.randint(1, med) > args.coverage:
return None, None
return name, seq
# the filtering loop
for infile in infiles:
print('filtering', infile)
outfile = os.path.basename(infile) + '.medfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(infile), outfp)
print('output in', outfile)
def test_maxcount_with_bigcount_save():
# hashtable should not saturate, if use_bigcount is set.
kh = khmer.Countgraph(4, 4**4, 4)
kh.set_use_bigcount(True)
for _ in range(0, 1000):
kh.count('AAAA')
c = kh.get('AAAA')
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
try:
kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
c = kh.get('AAAA')
assert c == 1000, "should be able to count to 1000: %d" % c
assert c != MAX_COUNT, c
def test_maxcount_with_bigcount_save():
# hashtable should not saturate, if use_bigcount is set.
kh = khmer.Countgraph(4, 4 ** 4, 4)
kh.set_use_bigcount(True)
for _ in range(0, 1000):
kh.count('AAAA')
c = kh.get('AAAA')
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
try:
kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
c = kh.get('AAAA')
assert c == 1000, "should be able to count to 1000: %d" % c
assert c != MAX_COUNT, c
def test_normalize_by_median_no_bigcount():
infile = utils.get_temp_filename("test.fa")
hashfile = utils.get_temp_filename("test-out.ct")
outfile = infile + ".keep"
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data("test-abund-read-2.fa"), infile)
counting_ht = _make_counting(infile, K=8)
script = "normalize-by-median.py"
args = ["-C", "1000", "-k 8", "--savegraph", hashfile, infile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0, (out, err)
print((out, err))
assert os.path.exists(hashfile), hashfile
kh = khmer.load_countgraph(hashfile)
assert kh.get("GGTTGACG") == 255
def test_nobigcount_save():
kh = khmer.Countgraph(4, 4 ** 4, 4)
# kh.set_use_bigcount(False) <-- this is the default
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
try:
kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
# set_use_bigcount should still be False after load (i.e. should be saved)
assert kh.get('AAAA') == 0
for _ in range(0, 1000):
kh.count('AAAA')
kh.get('AAAA')
assert kh.get('AAAA') == MAX_COUNT
def test_load_gz_truncated_should_fail():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
hi = khmer.Countgraph(12, 1000, 2)
hi.consume_seqfile(inpath)
hi.save(savepath)
fp = open(savepath, 'rb')
data = fp.read()
fp.close()
fp = open(savepath, 'wb')
fp.write(data[:1000])
fp.close()
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
def test_nobigcount_save():
kh = khmer.Countgraph(4, 4**4, 4)
# kh.set_use_bigcount(False) <-- this is the default
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
try:
kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
# set_use_bigcount should still be False after load (i.e. should be saved)
assert kh.get('AAAA') == 0
for _ in range(0, 1000):
kh.count('AAAA')
kh.get('AAAA')
assert kh.get('AAAA') == MAX_COUNT
def test_load_gz_truncated_should_fail():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
hi = khmer.Countgraph(12, 1000, 2)
hi.consume_fasta(inpath)
hi.save(savepath)
fp = open(savepath, 'rb')
data = fp.read()
fp.close()
fp = open(savepath, 'wb')
fp.write(data[:1000])
fp.close()
try:
hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
def test_bigcount_save():
# hashtable should not saturate, if use_bigcount is set.
kh = khmer.Countgraph(4, 4**4, 4)
kh.set_use_bigcount(True)
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
try:
kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
# set_use_bigcount should still be True after load (i.e. should be saved)
assert kh.get('AAAA') == 0
for _ in range(0, 1000):
kh.count('AAAA')
kh.get('AAAA')
assert kh.get('AAAA') == 1000
def test_save_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave2.ht.gz')
sizes = list(PRIMES_1m)
sizes.append(1000005)
hi = khmer._Countgraph(12, sizes)
hi.consume_seqfile(inpath)
hi.save(savepath)
try:
ht = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
tracking = khmer._Nodegraph(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
tracking = khmer._Nodegraph(12, sizes)
y = ht.abundance_distribution(inpath, tracking)
assert sum(x) == 3966, sum(x)
assert x == y, (x, y)
