def collapse(table: biom.Table,
mapping: str,
normalize: bool = False) -> biom.Table:
"""Collapse a feature table based on many-to-many mapping.
"""
with open(mapping, 'r') as fh:
mapping = read_map_many(fh)
table = collapse_biom(table, mapping, normalize)
table.generated_by = f'{__name__}-{__version__}'
return table
def coverage(table: biom.Table,
mapping: str,
threshold: int = None,
count: bool = False) -> biom.Table:
"""Calculate a feature table's coverage over feature groups.
"""
with open(mapping, 'r') as fh:
mapping = dict(read_map_all(fh))
table = calc_coverage(table, mapping, threshold, count)
table = table_to_biom(*table)
table.generated_by = f'{__name__}-{__version__}'
return table
def filter_table(table: biom.Table,
min_count: int = None,
min_percent: float = None) -> biom.Table:
"""Filter a feature table by per-sample abundance of features.
"""
# validate parameters
if not any((min_count, min_percent)):
raise ValueError('Please specify either minimum count or minimum '
'percentage threshold.')
if all((min_count, min_percent)):
raise ValueError('Only one of minimum count or minimum percentage '
'thresholds can be specified.')
if min_percent and min_percent >= 100:
raise ValueError('Minimum percentage threshold must be below 100.')
# determine threshold
th = min_count or min_percent / 100
# filter feature table
table = filter_biom(table, th)
table.generated_by = f'{__name__}-{__version__}'
return table
