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biom-format.org

Quick start

«  The biom file format: Version 2.1   ::   Contents   ::   biom.load_table  »

Quick start

BIOM has an example table and two methods for reading in Table objects that are immediately available at the package 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 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') 

«  The biom file format: Version 2.1   ::   Contents   ::   biom.load_table  »