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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 (file_reading_handler,
string_list_handler)
from biom.commands.metadata_adder import CommandConstructor
from biom.interfaces.optparse.input_handler import load_biom_table
from biom.interfaces.optparse.output_handler import write_biom_table
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso", "Morgan Langille",
"Daniel McDonald"]
__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="Adding sample metadata",
LongDesc="Add sample metadata to a BIOM table",
Ex="%prog -i otu_table.biom -o "
"table_with_sample_metadata.biom -m "
"sample_metadata.txt")
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type='existing_filepath',
Handler=load_biom_table, ShortName='i',
Name='input-fp'),
OptparseOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='existing_filepath',
Handler=file_reading_handler, ShortName='m',
Name='sample-metadata-fp'),
OptparseOption(Parameter=cmd_in_lookup('observation_metadata'),
Type='existing_filepath',
Handler=file_reading_handler,
Name='observation-metadata-fp'),
OptparseOption(Parameter=cmd_in_lookup('sc_separated'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to split '
'on semicolons. This is useful for hierarchical data such '
'as taxonomy or functional categories'),
OptparseOption(Parameter=cmd_in_lookup('sc_pipe_separated'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to split '
'on semicolons and pipes ("|"). This is useful for '
'hierarchical data such as functional categories with '
'one-to-many mappings (e.g. x;y;z|x;y;w)'),
OptparseOption(Parameter=cmd_in_lookup('int_fields'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to cast '
'to integers. This is useful for integer data such as '
'"DaysSinceStart"'),
OptparseOption(Parameter=cmd_in_lookup('float_fields'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to cast '
'to floating point numbers. This is useful for real number '
'data such as "pH"'),
OptparseOption(Parameter=cmd_in_lookup('sample_header'),
Handler=string_list_handler,
Help='comma-separated list of the sample metadata field '
'names. This is useful if a header line is not provided '
'with the metadata, if you want to rename the fields, or '
'if you want to include only the first n fields where n is '
'the number of entries provided here'),
OptparseOption(Parameter=cmd_in_lookup('observation_header'),
Handler=string_list_handler,
Help='comma-separated list of the observation metadata '
'field names. This is useful if a header line is not '
'provided with the metadata, if you want to rename the '
'fields, or if you want to include only the first n fields '
'where n is the number of entries provided here'),
OptparseOption(Parameter=cmd_in_lookup('output_as_json'),
Type=None,
Action='store_true'),
OptparseOption(Parameter=None, Type='new_filepath', ShortName='o',
Name='output-fp', Required=True,
Help='the output BIOM table')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('table'),
Handler=write_biom_table,
InputName='output-fp')
]
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