def test_extract_countgraph_info_badfile():
try:
khmer.extract_countgraph_info(
utils.get_test_data('test-abund-read-2.fa'))
assert 0, 'this should fail'
except ValueError:
pass
def test_extract_countgraph_info_badfile():
try:
khmer.extract_countgraph_info(
utils.get_test_data('test-abund-read-2.fa'))
assert 0, 'this should fail'
except ValueError:
pass
def check_conflicting_args(args, hashtype):
"""
Check argparse args object for conflicts.
e.g. --loadgraph and --ksize being set.
"""
if getattr(args, "quiet", None):
configure_logging(args.quiet)
loadgraph_table_conflicts = {
"ksize": DEFAULT_K,
"n_tables": DEFAULT_N_TABLES,
"max_tablesize": DEFAULT_MAX_TABLESIZE
}
loadgraph_autoarg_conflicts = ("unique_kmers", "max_memory_usage")
if getattr(args, "loadgraph", None):
# check for table config args
for key, value in loadgraph_table_conflicts.items():
if getattr(args, key, value) != value:
log_warn('''
*** WARNING: You are loading a saved k-mer countgraph from
*** {hashfile}, but have set k-mer table parameters.
*** Your values for ksize, n_tables, and tablesize
*** will be ignored.'''.format(hashfile=args.loadgraph))
break # no repeat warnings
for element in loadgraph_autoarg_conflicts:
if getattr(args, element, None):
log_warn("\n*** WARNING: You have asked that the graph size be"
" automatically calculated\n"
"*** (by using -U or -M).\n"
"*** But you are loading an existing graph!\n"
"*** Size will NOT be set automatically.")
break # no repeat warnings
infoset = None
if hashtype in ('countgraph', 'smallcountgraph'):
infoset = extract_countgraph_info(args.loadgraph)
if infoset is not None:
ksize = infoset.ksize
max_tablesize = infoset.table_size
n_tables = infoset.n_tables
args.ksize = ksize
args.n_tables = n_tables
args.max_tablesize = max_tablesize
if infoset.ht_type == khmer.FILETYPES['SMALLCOUNT']:
args.small_count = True
def check_conflicting_args(args, hashtype):
"""
Utility function that takes in an args object and checks if there's things
that conflict, e.g. --loadgraph and --ksize being set.
"""
if getattr(args, "quiet", None):
configure_logging(args.quiet)
loadgraph_table_conflicts = {
"ksize": DEFAULT_K,
"n_tables": DEFAULT_N_TABLES,
"max_tablesize": DEFAULT_MAX_TABLESIZE
}
loadgraph_autoarg_conflicts = ("unique_kmers", "max_memory_usage")
if getattr(args, "loadgraph", None):
# check for table config args
for key, value in loadgraph_table_conflicts.items():
if getattr(args, key, value) != value:
log_warn('''
*** WARNING: You are loading a saved k-mer countgraph from
*** {hashfile}, but have set k-mer table parameters.
*** Your values for ksize, n_tables, and tablesize
*** will be ignored.'''.format(hashfile=args.loadgraph))
break # no repeat warnings
for element in loadgraph_autoarg_conflicts:
if getattr(args, element, None):
log_warn("\n*** WARNING: You have asked that the graph size be"
" automatically calculated\n"
"*** (by using -U or -M).\n"
"*** But you are loading an existing graph!\n"
"*** Size will NOT be set automatically.")
break # no repeat warnings
infoset = None
if hashtype == 'countgraph':
infoset = extract_countgraph_info(args.loadgraph)
if info:
ksize = infoset[0]
max_tablesize = infoset[1]
n_tables = infoset[2]
args.ksize = ksize
args.n_tables = n_tables
args.max_tablesize = max_tablesize
def check_conflicting_args(args, hashtype):
"""
Check argparse args object for conflicts.
e.g. --loadgraph and --ksize being set.
"""
if getattr(args, "quiet", None):
configure_logging(args.quiet)
loadgraph_table_conflicts = {"ksize": DEFAULT_K,
"n_tables": DEFAULT_N_TABLES,
"max_tablesize": DEFAULT_MAX_TABLESIZE}
loadgraph_autoarg_conflicts = ("unique_kmers", "max_memory_usage")
if getattr(args, "loadgraph", None):
# check for table config args
for key, value in loadgraph_table_conflicts.items():
if getattr(args, key, value) != value:
log_warn('''
*** WARNING: You are loading a saved k-mer countgraph from
*** {hashfile}, but have set k-mer table parameters.
*** Your values for ksize, n_tables, and tablesize
*** will be ignored.'''.format(hashfile=args.loadgraph))
break # no repeat warnings
for element in loadgraph_autoarg_conflicts:
if getattr(args, element, None):
log_warn("\n*** WARNING: You have asked that the graph size be"
" automatically calculated\n"
"*** (by using -U or -M).\n"
"*** But you are loading an existing graph!\n"
"*** Size will NOT be set automatically.")
break # no repeat warnings
infoset = None
if hashtype in ('countgraph', 'smallcountgraph'):
infoset = extract_countgraph_info(args.loadgraph)
if infoset is not None:
ksize = infoset.ksize
max_tablesize = infoset.table_size
n_tables = infoset.n_tables
args.ksize = ksize
args.n_tables = n_tables
args.max_tablesize = max_tablesize
if infoset.ht_type == khmer.FILETYPES['SMALLCOUNT']:
args.small_count = True
def check_conflicting_args(args, hashtype):
"""
Utility function that takes in an args object and checks if there's things
that conflict, e.g. --loadgraph and --ksize being set.
"""
if getattr(args, "quiet", None):
configure_logging(args.quiet)
loadgraph_table_conflicts = {"ksize": DEFAULT_K,
"n_tables": DEFAULT_N_TABLES,
"max_tablesize": DEFAULT_MAX_TABLESIZE}
loadgraph_autoarg_conflicts = ("unique_kmers", "max_memory_usage")
if getattr(args, "loadgraph", None):
# check for table config args
for key, value in loadgraph_table_conflicts.items():
if getattr(args, key, value) != value:
log_warn('''
*** WARNING: You are loading a saved k-mer countgraph from
*** {hashfile}, but have set k-mer table parameters.
*** Your values for ksize, n_tables, and tablesize
*** will be ignored.'''.format(hashfile=args.loadgraph))
break # no repeat warnings
for element in loadgraph_autoarg_conflicts:
if getattr(args, element, None):
log_warn("\n*** WARNING: You have asked that the graph size be"
" automatically calculated\n"
"*** (by using -U or -M).\n"
"*** But you are loading an existing graph!\n"
"*** Size will NOT be set automatically.")
break # no repeat warnings
infoset = None
if hashtype == 'countgraph':
infoset = extract_countgraph_info(args.loadgraph)
if info:
ksize = infoset[0]
max_tablesize = infoset[1]
n_tables = infoset[2]
args.ksize = ksize
args.n_tables = n_tables
args.max_tablesize = max_tablesize
def test_extract_countgraph_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.Countgraph(25, size, 4)
ht.save(fn)
try:
info = khmer.extract_countgraph_info(fn)
except ValueError as err:
assert 0, 'Should not throw a ValueErorr: ' + str(err)
ksize, n_tables, table_size, _, _, _, _ = 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_countgraph_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
ht = khmer.Countgraph(25, size, 4)
ht.save(fn)
try:
info = khmer.extract_countgraph_info(fn)
except ValueError as err:
assert 0, 'Should not throw a ValueErorr: ' + str(err)
ksize, n_tables, table_size, _, _, _, _ = 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)
