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#!/usr/bin/env python
r"""
Quick start
===========
.. currentmodule:: biom
BIOM has an example table and two methods for reading in `Table` objects that
are immediately available at the package level.
Functions
---------
.. autosummary::
:toctree: generated/
load_table
Examples
--------
Load an example table:
>>> from biom import example_table
>>> print(example_table) # doctest: +NORMALIZE_WHITESPACE
# Constructed from biom file
#OTU ID S1 S2 S3
O1 0.0 1.0 2.0
O2 3.0 4.0 5.0
Parse a table from an open file object:
>>> from biom import parse_table
>>> with open('path/to/table.biom') as f: # doctest: +SKIP
... table = parse_table(f)
Parse a table from a path. BIOM will attempt to determine if the file is
either in TSV, HDF5, JSON, gzip'd JSON or gzip'd TSV and parse accordingly:
>>> from biom import load_table
>>> table = load_table('path/to/table.biom') # doctest: +SKIP
"""
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2020, 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 .table import Table
from .parse import parse_biom_table as parse_table, load_table, save_table
from .util import __format_version__, __version__
from ._subsample import subsample
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
"Jose Clemente", "Justin Kuczynski", "Antonio Gonzalez",
"Yoshiki Vazquez Baeza", "Jose Navas", "Adam Robbins-Pianka",
"Rob Knight", "Joshua Shorenstein", "Emily TerAvest",
"Michael Shaffer", "Qiyun Zhu", "Matt Aton"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Daniel McDonald"
__email__ = "daniel.mcdonald@colorado.edu"
example_table = Table([[0, 1, 2], [3, 4, 5]], ['O1', 'O2'],
['S1', 'S2', 'S3'],
[{'taxonomy': ['Bacteria', 'Firmicutes']},
{'taxonomy': ['Bacteria', 'Bacteroidetes']}],
[{'environment': 'A'},
{'environment': 'B'},
{'environment': 'A'}], input_is_dense=True)
def concat(tables, *args, **kwargs):
"""Wrapper for biom.Table.concat which requires a table instance
Parameters
----------
tables : iterable of biom.Table, or a single biom.Table instance
Tables to concatenate
Raises
------
DisjointIDError
If IDs over the axis are not disjoint.
Returns
-------
biom.Table
A table object reflecting the concatenation of the tables.
"""
return tables[0].concat(tables[1:], *args, **kwargs)
__all__ = ['Table', 'example_table', 'parse_table', 'load_table',
'__format_version__', '__version__', 'save_table',
'subsample']
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