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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 click
from biom import load_table
from biom.cli import cli
@cli.command()
@click.option('-i', '--input-fp', required=True,
type=click.Path(exists=True, dir_okay=False),
help='The input BIOM table')
@click.option('-o', '--output-fp', default=None,
type=click.Path(writable=True),
help='An output file-path', required=False)
@click.option('-n', '--n-obs', default=5, type=int,
help="The number of observations to show",
required=False)
@click.option('-m', '--n-samp', default=5, type=int,
help="The number of samples to show",
required=False)
def head(input_fp, output_fp, n_obs, n_samp):
"""Dump the first bit of a table.
Example usage:
Print out the upper left corner of a BIOM table to standard out:
$ biom head -i table.biom
"""
table = load_table(input_fp).head(n=n_obs, m=n_samp)
if output_fp is None:
click.echo(str(table))
else:
with open(output_fp, 'w') as fp:
fp.write(str(table))
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