biom.table.Table.to_tsv

Table.to_tsv(header_key=None, header_value=None, metadata_formatter=<class 'str'>, observation_column_name='#OTU ID', direct_io=None)

Return self as a string in tab delimited form

Default str output for the Table is just row/col ids and table data without any metadata

Parameters:

header_keystr or None, optional

Defaults to None

header_valuestr or None, optional

Defaults to None

metadata_formatterfunction, optional

Defaults to str. a function which takes a metadata entry and returns a formatted version that should be written to file

observation_column_namestr, optional

Defaults to “#OTU ID”. The name of the first column in the output table, corresponding to the observation IDs.

direct_iofile or file-like object, optional

Defaults to None. Must implement a write function. If direct_io is not None, the final output is written directly to direct_io during processing.

Returns:

str

tab delimited representation of the Table

Examples

>>> import numpy as np
>>> from biom.table import Table

Create a 2x3 BIOM table, with observation metadata and no sample metadata:

>>> data = np.asarray([[0, 0, 1], [1, 3, 42]])
>>> table = Table(data, ['O1', 'O2'], ['S1', 'S2', 'S3'],
...               [{'foo': 'bar'}, {'x': 'y'}], None)
>>> print(table.to_tsv()) 
# Constructed from biom file
#OTU ID S1      S2      S3
O1      0.0     0.0     1.0
O2      1.0     3.0     42.0
>>> with open("result.tsv", "w") as f:
        table.to_tsv(direct_io=f)