BIOM has an example table and two methods for reading in Table objects that are immediately available at the package level.
Load an example table:
>>> from biom import example_table >>> print example_table # Constructed from biom file #OTU ID S1 S2 S3 O1 0.0 1.0 2.0 O2 3.0 4.0 5.0
Parse a table from an open file object:
>>> from biom import parse_table >>> with open('path/to/table.biom') as f: ... table = parse_table(f)
Parse a table from a path. BIOM will attempt to determine if the file is either in TSV, HDF5, JSON, gzip’d JSON or gzip’d TSV and parse accordingly:
>>> from biom import load_table >>> table = load_table('path/to/table.biom')