def choose_cluster_subsets(otu_table_f, map_f, category, num_total_samples):
otu_table = parse_biom_table(otu_table_f)
metadata_map = MetadataMap.parseMetadataMap(map_f)
# Dirty... :(
try:
map_f.seek(0)
except AttributeError:
pass
if num_total_samples > len(otu_table.SampleIds):
raise InvalidSubsetSize("Too many total samples (%d) were specified "
"as a subset size. There are only %d total "
"samples to choose a subset from." %
(num_total_samples, len(otu_table.SampleIds)))
category_map = defaultdict(list)
for samp_id in metadata_map.SampleIds:
# Mapping files can have more samples than OTU tables.
if samp_id in otu_table.SampleIds:
category_val = metadata_map.getCategoryValue(samp_id, category)
category_map[category_val].append(samp_id)
samp_ids_to_keep, extra_samps = _choose_items_from_clusters(
category_map, otu_table.SampleIds, num_total_samples)
samp_ids_to_keep.extend(extra_samps)
assert len(samp_ids_to_keep) == num_total_samples, \
"%d != %d" % (len(samp_ids_to_keep), num_total_samples)
assert len(samp_ids_to_keep) == len(set(samp_ids_to_keep)), \
"Duplicate sample IDs in subset"
return (filter_samples_from_otu_table(otu_table, samp_ids_to_keep, 0, inf),
filter_mapping_file_from_mapping_f(map_f, samp_ids_to_keep))
def choose_gradient_subset(otu_table_f, map_f, category, num_total_samples):
otu_table = parse_biom_table(otu_table_f)
mdm, _ = parse_mapping_file_to_dict(map_f)
try:
map_f.seek(0)
except AttributeError:
pass
if num_total_samples > len(otu_table.SampleIds):
raise InvalidSubsetSize("Too many total samples (%d) were specified "
"as a gradient subset size. There are only %d "
"total samples to choose a subset from." %
(num_total_samples, len(otu_table.SampleIds)))
# Only keep the sample IDs that are in both the mapping file and OTU table.
# Sort the samples according to the gradient category.
samp_ids = [(samp_id, float(metadata[category]))
for samp_id, metadata in mdm.items()
if samp_id in otu_table.SampleIds]
samp_ids.sort(key=lambda samp_id: samp_id[1])
samp_ids_to_keep = [samp_id[0] for samp_id in
_choose_items_from_bins(samp_ids, num_total_samples)]
assert len(samp_ids_to_keep) == num_total_samples, \
"%d != %d" % (len(samp_ids_to_keep), num_total_samples)
assert len(samp_ids_to_keep) == len(set(samp_ids_to_keep)), \
"Duplicate sample IDs in subset"
return (filter_samples_from_otu_table(otu_table, samp_ids_to_keep, 0, inf),
filter_mapping_file_from_mapping_f(map_f, samp_ids_to_keep))
