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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__ = "Evan Bolyen"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Evan Bolyen", "Greg Caporaso", "Jai Ram Rideout"]
__license__ = "BSD"
__maintainer__ = "Evan Bolyen"
__email__ = "ebolyen@gmail.com"
import json
from biom.parse import MetadataMap, parse_biom_table
def load_biom_table(table_f):
"""Return a parsed BIOM table."""
return parse_biom_table(table_f)
def load_biom_table_with_file_contents(biom_f):
"""Return a BIOM table and the original open filehandle as a tuple.
Useful when additional computation needs to be performed on the file
contents, such as an MD5 sum.
WARNING: this function does not close the open filehandle that it returns.
Users of this function are responsible for closing the filehandle when done
using it!
"""
table = parse_biom_table(biom_f)
if hasattr(biom_f, 'seek'):
biom_f.seek(0)
return table, biom_f
def load_json_document(f):
"""Return a parsed JSON object."""
return json.load(f)
def load_metadata(lines):
"""Parse a sample/observation metadata file, return a ``MetadataMap``.
If ``lines`` is ``None``, this function will return ``None``.
"""
if lines is not None:
return MetadataMap.from_file(lines)
return None
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