Quick start¶
BIOM has an example table and two methods for reading in Table objects that are immediately available at the project level.
Functions¶
load_table(f) | Load a Table from a path |
Examples¶
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 fhe 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')