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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.
# ----------------------------------------------------------------------------
from __future__ import division
import biom.util
import biom.parse
def write_biom_table(table, fmt, filepath):
"""Write table in specified format to filepath"""
if fmt not in ['hdf5', 'json', 'tsv']:
raise ValueError("Unknown file format")
if fmt == 'hdf5' and not biom.util.HAVE_H5PY:
fmt = 'json'
if fmt == 'json':
with open(filepath, 'w') as f:
f.write(table.to_json(biom.parse.generatedby()))
elif fmt == 'tsv':
with open(filepath, 'w') as f:
f.write(table)
f.write('\n')
else:
import h5py
with h5py.File(filepath, 'w') as f:
table.to_hdf5(f, biom.parse.generatedby())
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