biom.table.Table.to_tsv¶
- Table.to_tsv(header_key=None, header_value=None, metadata_formatter=<type 'str'>, observation_column_name='#OTU ID')¶
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_key : str or None, optional
Defaults to None
header_value : str or None, optional
Defaults to None
metadata_formatter : function, optional
Defaults to str. a function which takes a metadata entry and returns a formatted version that should be written to file
observation_column_name : str, optional
Defaults to “#OTU ID”. The name of the first column in the output table, corresponding to the observation IDs.
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