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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.
# ----------------------------------------------------------------------------
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.optparse.input_handler import load_file_lines
from biom.interfaces.optparse.input_handler import biom_load_file_contents
from biom.interfaces.optparse.output_handler import write_subsetted_biom_table
from biom.commands.table_subsetter import CommandConstructor
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Daniel McDonald",
"Jose Antonio Navas Molina"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Subsetting a json BIOM table",
LongDesc="Choose a subset of the observations in "
"table.biom and write them to subset.biom",
Ex="%prog -j table.biom -a observations -s "
"observation_ids.txt -o subset.biom"),
OptparseUsageExample(ShortDesc="Subsetting a hdf5 BIOM table",
LongDesc="Choose a subset of the observations in "
"table.biom and write them to subset.biom",
Ex="%prog -i table.biom -a observations -s "
"observation_ids.txt -o subset.biom")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('hdf5_table'),
Type='existing_filepath',
Handler=None, ShortName='i',
Name='input-hdf5-fp',
Help='the input hdf5 BIOM table filepath to subset'),
OptparseOption(Parameter=cmd_in_lookup('json_table_str'),
Type='existing_filepath',
Handler=biom_load_file_contents, ShortName='j',
Name='input-json-fp',
Help='the input hdf5 BIOM table filepath to subset'),
OptparseOption(Parameter=cmd_in_lookup('axis'), ShortName='a'),
OptparseOption(Parameter=cmd_in_lookup('ids'),
Type='existing_filepath', Handler=load_file_lines,
ShortName='s', Help='a file containing a single column of '
'IDs to retain (either sample IDs or observation IDs, '
'depending on the axis)'),
OptparseOption(Parameter=None, Type='new_filepath', ShortName='o',
Name='output-fp', Required=True,
Help='the output BIOM table filepath'),
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('subsetted_table'),
Handler=write_subsetted_biom_table,
InputName='output-fp')
]
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