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# -----------------------------------------------------------------------------
# Copyright (c) 2011-2017, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
import click
from biom import load_table
from biom.cli import cli
@cli.command(name='export-metadata')
@click.option('-i', '--input-fp', required=True,
type=click.Path(exists=True, dir_okay=False),
help='The input BIOM table')
@click.option('-m', '--sample-metadata-fp', required=False,
type=click.Path(exists=False, dir_okay=False),
help='The sample metadata output file.')
@click.option('--observation-metadata-fp', required=False,
type=click.Path(exists=False, dir_okay=False),
help='The observation metadata output file.')
def export_metadata(input_fp, sample_metadata_fp, observation_metadata_fp):
"""Export metadata as TSV.
Example usage:
Export metadata as TSV:
$ biom export-metadata -i otu_table.biom
--sample-metadata-fp sample.tsv
--observation-metadata-fp observation.tsv
"""
table = load_table(input_fp)
if sample_metadata_fp:
_export_metadata(table, 'sample', input_fp, sample_metadata_fp)
if observation_metadata_fp:
_export_metadata(table, 'observation', input_fp,
observation_metadata_fp)
def _export_metadata(table, axis, input_fp, output_fp):
try:
metadata = table.metadata_to_dataframe(axis)
metadata.to_csv(output_fp, sep='\t')
except KeyError:
click.echo('File {} does not contain {} metadata'.format(input_fp,
axis))
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