# ----------------------------------------------------------------------------- # 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. # ----------------------------------------------------------------------------- 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) 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) 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