def write_rarefied_otu_table(**kwargs):
output_table_io = kwargs.pop('output_table_io')
table_collection = kwargs.pop('table_collection')
number_to_choose = kwargs.pop('number_to_choose', None)
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if number_to_choose is None:
counts = {}
for otu in table_collection:
key = "%s_singlem_RAND8_%s" % (otu.sample_name, otu.marker)
try:
counts[key] += otu.count
except KeyError:
counts[key] = otu.count
number_to_choose = min(counts.values())
logging.info(
"Minimum number of sequences detected is %i, rarefying all sample/gene combinations to this level"
% number_to_choose)
logging.info(
"Rarefying OTU table to max %i sequences per sample/gene combination and writing to %s"
% (number_to_choose, output_table_io.name))
OtuTable.write_otus_to(
Rarefier().rarefy(table_collection, number_to_choose),
output_table_io)
def write_otu_table(**kwargs):
output_table_io = kwargs.pop('output_table_io')
table_collection = kwargs.pop('table_collection')
output_extras = kwargs.pop('output_extras')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if hasattr(output_table_io, 'name'):
logging.info("Writing %s" % output_table_io.name)
else:
logging.info("Writing an OTU table")
if output_extras:
OtuTable.write_otus_to(table_collection, output_table_io,
fields_to_print=table_collection.example_field_names())
else:
OtuTable.write_otus_to(table_collection, output_table_io)
def write_otu_table(**kwargs):
output_table_io = kwargs.pop('output_table_io')
table_collection = kwargs.pop('table_collection')
output_extras = kwargs.pop('output_extras')
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if hasattr(output_table_io, 'name'):
logging.info("Writing %s" % output_table_io.name)
else:
logging.info("Writing an OTU table")
if output_extras:
OtuTable.write_otus_to(table_collection, output_table_io,
fields_to_print=table_collection.example_field_names())
else:
OtuTable.write_otus_to(table_collection, output_table_io)
def write_rarefied_otu_table(**kwargs):
output_table_io = kwargs.pop('output_table_io')
table_collection = kwargs.pop('table_collection')
number_to_choose = kwargs.pop('number_to_choose', None)
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
if number_to_choose is None:
counts = {}
for otu in table_collection:
key = "%s_singlem_RAND8_%s" % (otu.sample_name, otu.marker)
try:
counts[key] += otu.count
except KeyError:
counts[key] = otu.count
number_to_choose = min(counts.values())
logging.info("Minimum number of sequences detected is %i, rarefying all sample/gene combinations to this level" % number_to_choose)
logging.info("Rarefying OTU table to max %i sequences per sample/gene combination and writing to %s" % (number_to_choose, output_table_io.name))
OtuTable.write_otus_to(Rarefier().rarefy(table_collection, number_to_choose),
output_table_io)