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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", "Daniel McDonald"]
__license__ = "BSD"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.optparse import (OptparseOption,
OptparseUsageExample,
OptparseResult)
from pyqi.core.interfaces.optparse.output_handler import (
write_or_print_list_of_strings)
from biom.commands.table_summarizer import CommandConstructor
from biom.interfaces.optparse.input_handler import (
load_biom_table_with_file_contents)
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Basic script usage",
LongDesc="Write a summary of table.biom to "
"table_summary.txt",
Ex="%prog -i table.biom -o table_summary.txt")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type="existing_filepath",
Handler=load_biom_table_with_file_contents,
ShortName='i',
Name='input-fp'),
OptparseOption(Parameter=cmd_in_lookup('qualitative'),
Type=None,
Action="store_true"),
OptparseOption(Parameter=cmd_in_lookup('observations'),
Type=None,
Action='store_true'),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=False,
Default=None,
Help='the output filepath')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('biom_summary'),
Handler=write_or_print_list_of_strings,
InputName='output-fp')
]
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