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#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2013, 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.
# ----------------------------------------------------------------------------
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
__license__ = "BSD"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from os.path import exists
from pyqi.core.exception import IncompetentDeveloperError
from pyqi.core.interfaces.optparse.output_handler import write_list_of_strings
from biom.parse import generatedby
from biom.util import HAVE_H5PY
def write_subsetted_biom_table(result_key, data, option_value=None):
"""Write a string to a file"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without a "
"filepath.")
if exists(option_value):
raise IOError("Output path '%s' already exists." % option_value)
table, fmt = data
if fmt not in ['hdf5', 'json']:
raise IncompetentDeveloperError("Unknown file format")
if fmt == 'json':
write_list_of_strings(result_key, table, option_value)
else:
if HAVE_H5PY:
import h5py
else:
# This should never be raised here
raise ImportError("h5py is not available, cannot write HDF5!")
with h5py.File(option_value, 'w') as f:
table.to_hdf5(f, generatedby())
def write_biom_table(result_key, data, option_value=None):
"""Write a string to a file"""
if option_value is None:
raise IncompetentDeveloperError("Cannot write output without a "
"filepath.")
if exists(option_value):
raise IOError("Output path '%s' already exists." % option_value)
table, fmt = data
if fmt not in ['hdf5', 'json', 'tsv']:
raise IncompetentDeveloperError("Unknown file format")
if fmt == 'json':
with open(option_value, 'w') as f:
f.write(table.to_json(generatedby()))
elif fmt == 'tsv':
with open(option_value, 'w') as f:
f.write(table)
f.write('\n')
else:
if HAVE_H5PY:
import h5py
else:
raise ImportError("h5py is not available, cannot write HDF5!")
with h5py.File(option_value, 'w') as f:
table.to_hdf5(f, generatedby())
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