def get_rare_data(otu_table,
seqs_per_sample,
include_small_samples=False,
subsample_f=subsample):
"""Filter OTU table to keep only desired sample sizes.
- include_small_sampes=False => do not write samples with < seqs_per_sample
total sequecnes
- otu_table (input and out) is otus(rows) by samples (cols)
- no otus are removed, even if they are absent in the rarefied table"""
with errstate(empty='raise'):
if not include_small_samples:
otu_table = filter_samples_from_otu_table(otu_table,
otu_table.ids(),
seqs_per_sample, inf)
# subsample samples that have too many sequences
def func(x, s_id, s_md):
if x.sum() < seqs_per_sample:
return x
else:
return subsample_f(x.astype(int), seqs_per_sample)
subsampled_otu_table = otu_table.transform(func, axis='sample')
return subsampled_otu_table
def get_rare_data(otu_table,
seqs_per_sample,
include_small_samples=False,
subsample_f=subsample):
"""Filter OTU table to keep only desired sample sizes.
- include_small_sampes=False => do not write samples with < seqs_per_sample
total sequecnes
- otu_table (input and out) is otus(rows) by samples (cols)
- no otus are removed, even if they are absent in the rarefied table"""
with errstate(empty='raise'):
if not include_small_samples:
otu_table = filter_samples_from_otu_table(
otu_table,
otu_table.ids(),
seqs_per_sample,
inf)
# subsample samples that have too many sequences
def func(x, s_id, s_md):
if x.sum() < seqs_per_sample:
return x
else:
return subsample_f(x.astype(int), seqs_per_sample)
subsampled_otu_table = otu_table.transform(func, axis='sample')
return subsampled_otu_table
def split_otu_table_on_sample_metadata(otu_table, mapping_f, mapping_field):
""" split otu table into sub otu tables where each represent samples
corresponding to only a certain value in mapping_field
"""
with errstate(empty='raise'):
mapping_f = list(mapping_f)
mapping_values = get_mapping_values(mapping_f, mapping_field)
tables = 0
for v in mapping_values:
v_fp_str = v.replace(' ', '_')
sample_ids_to_keep = sample_ids_from_metadata_description(
mapping_f, valid_states_str="%s:%s" % (mapping_field, v))
try:
# filtering cannot be inplace otherwise we lose data
filtered_otu_table = otu_table.filter(
lambda values, id_, metadata: id_ in sample_ids_to_keep,
axis='sample', inplace=False)
tables += 1
except TableException:
# all samples are filtered out, so no otu table to write
continue
yield v_fp_str, filtered_otu_table
if not tables:
raise OTUTableSplitError(
"Could not split OTU tables! There are no matches between the "
"sample identifiers in the OTU table and the mapping file.")
def test_errstate(self):
def foo(item):
return "the callback called"
table = Table([], [], [])
seterrcall('empty', foo)
self.assertNotEqual(geterr()['empty'], 'call')
with errstate(empty='call'):
result = errcheck(table)
self.assertEqual(result, "the callback called")
self.assertNotEqual(geterr()['empty'], 'call')
