biom.table.Table.from_adjacency¶

static Table.from_adjacency(lines)¶

Parse an adjacency format into BIOM

Parameters:

lineslist, str, or file-like object: The tab delimited data to parse

Returns:

biom.Table: A BIOM Table object

Raises:

ValueError: If the input is not an iterable or file-like object.
ValueError: If the data is incorrectly formatted.

Notes

The input is expected to be of the form: observation, sample, value. A header is not required, but if present, it must be of the form:

#OTU ID<tab>SampleID<tab>value

Examples

Parse tab separated adjacency data into a table:

>>> from biom.table import Table
>>> from io import StringIO
>>> data = 'a\tb\t1\na\tc\t2\nd\tc\t3'
>>> data_fh = StringIO(data)
>>> test_table = Table.from_adjacency(data_fh)