def test_extract_countinghash_info_badfile():
try:
khmer.extract_countinghash_info(
utils.get_test_data('test-abund-read-2.fa'))
assert 0, 'this should fail'
except ValueError:
pass
def __call__(self, parser, namespace, values, option_string=None):
env_ksize = os.environ.get('KHMER_KSIZE', DEFAULT_K)
env_n_tables = os.environ.get('KHMER_N_TABLES', DEFAULT_N_TABLES)
env_tablesize = os.environ.get('KHMER_MIN_TABLESIZE',
DEFAULT_MIN_TABLESIZE)
from khmer.utils import print_error
setattr(namespace, self.dest, values)
if getattr(namespace, 'ksize') != env_ksize or \
getattr(namespace, 'n_tables') != env_n_tables or \
getattr(namespace, 'min_tablesize') != env_tablesize:
if values:
print_error('''
** WARNING: You are loading a saved k-mer table from
{hashfile}, but have set k-mer table parameters.
Your values for ksize, n_tables, and tablesize
will be ignored.'''.format(hashfile=values))
if hasattr(parser, 'hashtype'):
info = None
if parser.hashtype == 'hashbits':
info = extract_hashbits_info(
getattr(namespace, self.dest))
elif parser.hashtype == 'counting':
info = extract_countinghash_info(
getattr(namespace, self.dest))
if info:
K = info[0]
x = info[1]
n = info[2]
setattr(namespace, 'ksize', K)
setattr(namespace, 'n_tables', n)
setattr(namespace, 'min_tablesize', x)
def __call__(self, parser, namespace, values, option_string=None):
env_ksize = os.environ.get('KHMER_KSIZE', DEFAULT_K)
env_n_tables = os.environ.get('KHMER_N_TABLES', DEFAULT_N_TABLES)
env_tablesize = os.environ.get('KHMER_MIN_TABLESIZE',
DEFAULT_MIN_TABLESIZE)
from khmer.utils import print_error
setattr(namespace, self.dest, values)
if getattr(namespace, 'ksize') != env_ksize or \
getattr(namespace, 'n_tables') != env_n_tables or \
getattr(namespace, 'min_tablesize') != env_tablesize:
if values:
print_error('''
** WARNING: You are loading a saved k-mer table from
{hashfile}, but have set k-mer table parameters.
Your values for ksize, n_tables, and tablesize
will be ignored.'''.format(hashfile=values))
if hasattr(parser, 'hashtype'):
info = None
if parser.hashtype == 'hashbits':
info = extract_hashbits_info(getattr(namespace, self.dest))
elif parser.hashtype == 'counting':
info = extract_countinghash_info(
getattr(namespace, self.dest))
if info:
K = info[0]
x = info[1]
n = info[2]
setattr(namespace, 'ksize', K)
setattr(namespace, 'n_tables', n)
setattr(namespace, 'min_tablesize', x)
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, values)
if getattr(namespace, 'ksize') != DEFAULT_K or \
getattr(namespace, 'n_tables') != DEFAULT_N_TABLES or \
getattr(namespace, 'max_tablesize') != DEFAULT_MAX_TABLESIZE:
if values:
print_error('''
** WARNING: You are loading a saved k-mer table from
** {hashfile}, but have set k-mer table parameters.
** Your values for ksize, n_tables, and tablesize
** will be ignored.'''.format(hashfile=values))
if hasattr(parser, 'hashtype'):
info = None
if parser.hashtype == 'nodegraph':
info = extract_hashbits_info(
getattr(namespace, self.dest))
elif parser.hashtype == 'countgraph':
info = extract_countinghash_info(
getattr(namespace, self.dest))
if info:
K = info[0]
x = info[1]
n = info[2]
setattr(namespace, 'ksize', K)
setattr(namespace, 'n_tables', n)
setattr(namespace, 'max_tablesize', x)
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, values)
if getattr(namespace, 'ksize') != DEFAULT_K or \
getattr(namespace, 'n_tables') != DEFAULT_N_TABLES or \
getattr(namespace, 'max_tablesize') != DEFAULT_MAX_TABLESIZE:
if values:
print_error('''
** WARNING: You are loading a saved k-mer table from
** {hashfile}, but have set k-mer table parameters.
** Your values for ksize, n_tables, and tablesize
** will be ignored.'''.format(hashfile=values))
if hasattr(parser, 'hashtype'):
info = None
if parser.hashtype == 'nodegraph':
info = extract_hashbits_info(
getattr(namespace, self.dest))
elif parser.hashtype == 'countgraph':
info = extract_countinghash_info(
getattr(namespace, self.dest))
if info:
K = info[0]
x = info[1]
n = info[2]
setattr(namespace, 'ksize', K)
setattr(namespace, 'n_tables', n)
setattr(namespace, 'max_tablesize', x)
def test_extract_countinghash_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.new_counting_hash(25, size, 4)
ht.save(fn)
info = khmer.extract_countinghash_info(fn)
ksize, table_size, n_tables, _, _, _ = info
print ksize, table_size, n_tables
assert(ksize) == 25
assert table_size == size
assert n_tables == 4
try:
os.remove(fn)
except OSError as e:
print >>sys.stder, '...failed to remove {fn}'.format(fn)
def test_extract_countinghash_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.new_counting_hash(25, size, 4)
ht.save(fn)
info = khmer.extract_countinghash_info(fn)
ksize, table_size, n_tables, _, _, _ = info
print ksize, table_size, n_tables
assert(ksize) == 25
assert table_size == size
assert n_tables == 4
try:
os.remove(fn)
except OSError as e:
print >>sys.stder, '...failed to remove {fn}'.format(fn)
def test_extract_countinghash_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.new_counting_hash(25, size, 4)
ht.save(fn)
try:
info = khmer.extract_countinghash_info(fn)
except ValueError as err:
assert 0, 'Should not throw a ValueErorr: ' + str(err)
ksize, table_size, n_tables, _, _, _ = info
print(ksize, table_size, n_tables)
assert (ksize) == 25
assert table_size == size
assert n_tables == 4
try:
os.remove(fn)
except OSError as err:
assert 0, '...failed to remove ' + fn + str(err)
def test_extract_countinghash_info():
fn = utils.get_temp_filename("test_extract_counting.ct")
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.new_counting_hash(25, size, 4)
ht.save(fn)
try:
info = khmer.extract_countinghash_info(fn)
except ValueError as err:
assert 0, "Should not throw a ValueErorr: " + str(err)
ksize, table_size, n_tables, _, _, _ = info
print(ksize, table_size, n_tables)
assert (ksize) == 25
assert table_size == size
assert n_tables == 4
try:
os.remove(fn)
except OSError as err:
assert 0, "...failed to remove " + fn + str(err)
def __call__(self, parser, namespace, values, option_string=None):
env_ksize = os.environ.get("KHMER_KSIZE", DEFAULT_K)
env_n_tables = os.environ.get("KHMER_N_TABLES", DEFAULT_N_TABLES)
env_tablesize = os.environ.get("KHMER_MIN_TABLESIZE", DEFAULT_MIN_TABLESIZE)
from khmer.utils import print_error
setattr(namespace, self.dest, values)
if (
getattr(namespace, "ksize") != env_ksize
or getattr(namespace, "n_tables") != env_n_tables
or getattr(namespace, "min_tablesize") != env_tablesize
):
if values:
print_error(
"""
** WARNING: You are loading a saved k-mer table from
{hashfile}, but have set k-mer table parameters.
Your values for ksize, n_tables, and tablesize
will be ignored.""".format(
hashfile=values
)
)
if hasattr(parser, "hashtype"):
info = None
if parser.hashtype == "hashbits":
info = extract_hashbits_info(getattr(namespace, self.dest))
elif parser.hashtype == "counting":
info = extract_countinghash_info(getattr(namespace, self.dest))
if info:
K = info[0]
x = info[1]
n = info[2]
setattr(namespace, "ksize", K)
setattr(namespace, "n_tables", n)
setattr(namespace, "min_tablesize", x)
def test_extract_countinghash_info_badfile():
try:
khmer.extract_countinghash_info(utils.get_test_data("test-abund-read-2.fa"))
assert 0, "this should fail"
except ValueError:
pass
