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 create_countgraph(args, ksize=None, multiplier=1.0):
if ksize is None:
ksize = args.ksize
if ksize > 32:
print_error("\n** ERROR: khmer only supports k-mer sizes <= 32.\n")
sys.exit(1)
tablesize = _calculate_tablesize(args, 'countgraph', multiplier=multiplier)
return khmer.CountingHash(ksize, tablesize, args.n_tables)
def create_countgraph(args, ksize=None, multiplier=1.0):
if ksize is None:
ksize = args.ksize
if ksize > 32:
print_error("\n** ERROR: khmer only supports k-mer sizes <= 32.\n")
sys.exit(1)
tablesize = _calculate_tablesize(args, 'countgraph', multiplier=multiplier)
return khmer.CountingHash(ksize, tablesize, args.n_tables)
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 report_on_config(args):
"""
Summarizes the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if args.quiet:
return
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n hashes = {0} \t\t(-N)".format(args.n_hashes))
print_error(" - min hashsize = {0:5.2g} \t(-x)".format(args.min_hashsize))
print_error("")
print_error("Estimated memory usage is {0:.2g} bytes "
"(n_hashes x min_hashsize)".format(args.n_hashes *
args.min_hashsize))
print_error("-" * 8)
if DEFAULT_MIN_HASHSIZE == args.min_hashsize:
print_error("** WARNING: hashsize is default! "
"You absodefly want to increase this!\n** "
"Please read the docs!")
def report_on_config(args, hashtype='counting'):
"""Print out configuration.
Summarize the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if args.quiet:
return
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n tables = {0} \t\t(-N)".format(args.n_tables))
print_error(
" - min tablesize = {0:5.2g} \t(-x)".format(args.min_tablesize)
)
print_error("")
if hashtype == 'counting':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x min_tablesize)".format(
args.n_tables * args.min_tablesize))
elif hashtype == 'hashbits':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x min_tablesize / 8)".format(args.n_tables *
args.min_tablesize / 8)
)
print_error("-" * 8)
if DEFAULT_MIN_TABLESIZE == args.min_tablesize and \
not hasattr(args, 'loadtable'):
print_error(
"** WARNING: tablesize is default! "
"You absodefly want to increase this!\n** "
"Please read the docs!\n"
)
def report_on_config(args, hashtype='counting'):
"""
Summarizes the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if args.quiet:
return
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n tables = {0} \t\t(-N)".format(args.n_tables))
print_error(" - min tablesize = {0:5.2g} \t(-x)".format(
args.min_tablesize))
print_error("")
if hashtype == 'counting':
print_error("Estimated memory usage is {0:.2g} bytes "
"(n_tables x min_tablesize)".format(args.n_tables *
args.min_tablesize))
elif hashtype == 'hashbits':
print_error("Estimated memory usage is {0:.2g} bytes "
"(n_tables x min_tablesize / 8)".format(
args.n_tables * args.min_tablesize / 8))
print_error("-" * 8)
if DEFAULT_MIN_TABLESIZE == args.min_tablesize and \
not hasattr(args, 'loadtable'):
print_error("** WARNING: tablesize is default! "
"You absodefly want to increase this!\n** "
"Please read the docs!\n")
def report_on_config(args, hashtype='countgraph'):
"""Print out configuration.
Summarize the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if hashtype not in ('countgraph', 'nodegraph'):
raise Exception("unknown graph type: %s" % (hashtype,))
if args.quiet:
return
tablesize = _calculate_tablesize(args, hashtype)
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n tables = {0} \t\t(-N)".format(args.n_tables))
print_error(
" - max tablesize = {0:5.2g} \t(-x)".format(tablesize)
)
print_error("")
if hashtype == 'countgraph':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x max_tablesize)".format(
args.n_tables * tablesize))
elif hashtype == 'nodegraph':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x max_tablesize / 8)".format(args.n_tables *
tablesize / 8)
)
print_error("-" * 8)
if DEFAULT_MAX_TABLESIZE == tablesize and \
not getattr(args, 'loadtable', None):
print_error('''\
** WARNING: tablesize is default!
** You probably want to increase this with -M/--max-memory-usage!
** Please read the docs!
''')
def report_on_config(args, hashtype='countgraph'):
"""Print out configuration.
Summarize the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if hashtype not in ('countgraph', 'nodegraph'):
raise Exception("unknown graph type: %s" % (hashtype,))
if args.quiet:
return
tablesize = _calculate_tablesize(args, hashtype)
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n tables = {0} \t\t(-N)".format(args.n_tables))
print_error(
" - max tablesize = {0:5.2g} \t(-x)".format(tablesize)
)
print_error("")
if hashtype == 'countgraph':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x max_tablesize)".format(
args.n_tables * tablesize))
elif hashtype == 'nodegraph':
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_tables x max_tablesize / 8)".format(args.n_tables *
tablesize / 8)
)
print_error("-" * 8)
if DEFAULT_MAX_TABLESIZE == tablesize and \
not getattr(args, 'loadtable', None):
print_error('''\
** WARNING: tablesize is default!
** You probably want to increase this with -M/--max-memory-usage!
** Please read the docs!
''')
def report_on_config( args ):
"""
Summarizes the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
if args.quiet: return
print_error( "\nPARAMETERS:" )
print_error( " - kmer size = {0} \t\t(-k)".format( args.ksize ) )
print_error( " - n hashes = {0} \t\t(-N)".format( args.n_hashes ) )
print_error(
" - min hashsize = {0:5.2g} \t(-x)".format( args.min_hashsize )
)
print_error( "" )
print_error(
"Estimated memory usage is {0:.2g} bytes "
"(n_hashes x min_hashsize)".format( args.n_hashes * args.min_hashsize )
)
print_error( "-" * 8 )
if DEFAULT_MIN_HASHSIZE == args.min_hashsize:
print_error(
"** WARNING: hashsize is default! "
"You absodefly want to increase this!\n** "
"Please read the docs!"
)
