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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
from biom.cli.util import write_biom_table
from biom.parse import MetadataMap
table_types = ["OTU table",
"Pathway table",
"Function table",
"Ortholog table",
"Gene table",
"Metabolite table",
"Taxon table",
"Table"]
observation_metadata_types = {
'sc_separated': lambda x: [e.strip() for e in x.split(';')],
'naive': lambda x: x
}
observation_metadata_types['taxonomy'] = \
observation_metadata_types['sc_separated']
observation_metadata_formatters = {
'sc_separated': lambda x: '; '.join(x),
'naive': lambda x: x
}
@cli.command(name='convert')
@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', required=True,
type=click.Path(exists=False, dir_okay=False),
help='The output BIOM table')
@click.option('-m', '--sample-metadata-fp', required=False,
type=click.Path(exists=True, dir_okay=False),
help='The sample metadata mapping file (will add sample '
'metadata to the input BIOM table, if provided).')
@click.option('--observation-metadata-fp', required=False,
type=click.Path(exists=True, dir_okay=False),
help='The observation metadata mapping file (will add '
'observation metadata to the input BIOM table, if '
'provided).')
@click.option('--to-json', default=False, is_flag=True,
help='Output as JSON-formatted table.')
@click.option('--to-hdf5', default=False, is_flag=True,
help='Output as HDF5-formatted table.')
@click.option('--to-tsv', default=False, is_flag=True,
help='Output as TSV-formatted (classic) table.')
@click.option('--collapsed-samples', default=False, is_flag=True,
help='If --to_hdf5 is passed and the original table is a '
'BIOM table with collapsed samples, this will '
'update the sample metadata of the table to '
'the supported HDF5 collapsed format.')
@click.option('--collapsed-observations', default=False, is_flag=True,
help='If --to_hdf5 is passed and the original table is a '
'BIOM table with collapsed observations, this will '
'update the observation metadata of the table '
'to the supported HDF5 collapsed format.')
@click.option('--header-key', required=False, type=click.STRING,
help='The observation metadata to include from the input '
'BIOM table file when creating a tsv table file. '
'By default no observation metadata will be included.')
@click.option('--output-metadata-id', required=False, type=click.STRING,
help='The name to be given to the observation metadata '
'column when creating a tsv table file if the column '
'should be renamed.')
@click.option('--table-type', required=False,
type=click.Choice(table_types),
help='The type of the table.')
@click.option('--process-obs-metadata', required=False,
type=click.Choice(
observation_metadata_types),
help='Process metadata associated with observations when '
'converting from a classic table.')
@click.option('--tsv-metadata-formatter', required=False,
default='sc_separated',
type=click.Choice(
observation_metadata_formatters),
help='Method for formatting the observation metadata.')
def convert(input_fp, output_fp, sample_metadata_fp, observation_metadata_fp,
to_json, to_hdf5, to_tsv, collapsed_samples,
collapsed_observations, header_key, output_metadata_id, table_type,
process_obs_metadata, tsv_metadata_formatter):
"""Convert to/from the BIOM table format.
Convert between BIOM table formats. See examples here:
http://biom-format.org/documentation/biom_conversion.html
Example usage:
Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM
formatted OTU table:
$ biom convert -i table.txt -o table.biom --to-hdf5
"""
if sum([to_tsv, to_hdf5, to_json]) > 1:
raise ValueError("--to-tsv, --to-json, and --to-hdf5 are mutually "
"exclusive. You can only pass one of these options.")
table = load_table(input_fp)
if sample_metadata_fp is not None:
with open(sample_metadata_fp, 'U') as f:
sample_metadata_f = MetadataMap.from_file(f)
else:
sample_metadata_f = None
if observation_metadata_fp is not None:
with open(observation_metadata_fp, 'U') as f:
observation_metadata_f = MetadataMap.from_file(f)
else:
observation_metadata_f = None
_convert(table, output_fp, sample_metadata_f, observation_metadata_f,
to_json, to_hdf5, to_tsv, collapsed_samples,
collapsed_observations, header_key, output_metadata_id,
table_type, process_obs_metadata, tsv_metadata_formatter)
def _convert(table, output_filepath, sample_metadata=None,
observation_metadata=None, to_json=False, to_hdf5=False,
to_tsv=False, collapsed_samples=False,
collapsed_observations=False, header_key=None,
output_metadata_id=None, table_type=None,
process_obs_metadata=None, tsv_metadata_formatter='sc_separated'):
if sum([to_tsv, to_hdf5, to_json]) == 0:
raise ValueError("Must specify an output format")
elif sum([to_tsv, to_hdf5, to_json]) > 1:
raise ValueError("Can only specify a single output format")
if table_type is None:
if table.type in [None, "None"]:
table.type = "Table"
else:
pass
else:
table.type = table_type
if tsv_metadata_formatter is not None:
obs_md_fmt_f = observation_metadata_formatters[tsv_metadata_formatter]
if sample_metadata is not None:
table.add_metadata(sample_metadata)
# if the user does not specify a name for the output metadata column,
# set it to the same as the header key
output_metadata_id = output_metadata_id or header_key
if process_obs_metadata is not None and not to_tsv:
if table.metadata(axis='observation') is None:
raise ValueError("Observation metadata processing requested "
"but it doesn't appear that there is any "
"metadata to operate on!")
# and if this came in as TSV, then we expect only a single type of
# metadata
md_key = list(table.metadata(axis='observation')[0].keys())[0]
process_f = observation_metadata_types[process_obs_metadata]
it = zip(table.ids(axis='observation'),
table.metadata(axis='observation'))
new_md = {id_: {md_key: process_f(md[md_key])} for id_, md in it}
if observation_metadata:
for k, v in observation_metadata.items():
new_md[k].update(v)
table.add_metadata(new_md, 'observation')
if to_tsv:
result = table.to_tsv(header_key=header_key,
header_value=output_metadata_id,
metadata_formatter=obs_md_fmt_f)
with open(output_filepath, 'w') as f:
f.write(result)
return
elif to_json:
fmt = 'json'
result = table
elif to_hdf5:
fmt = 'hdf5'
result = table
if collapsed_observations:
metadata = [{'collapsed_ids': sorted(md.keys())}
for md in result.metadata(axis='observation')]
result._observation_metadata = metadata
if collapsed_samples:
metadata = [{'collapsed_ids': sorted(md.keys())}
for md in result.metadata()]
result._sample_metadata = metadata
if collapsed_observations or collapsed_samples:
# We have changed the metadata, it is safer to make sure that
# it is correct
result._cast_metadata()
write_biom_table(result, fmt, output_filepath)
return
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