def main():
opts,args = parser.parse_args()
if opts.input_fp is None:
parser.print_help()
parser.error('Must specify an input file!')
if opts.output_fp is None:
parser.print_help()
parser.error('Must specify an output file!')
biom_to_classic_table = opts.biom_to_classic_table
sparse_biom_to_dense_biom = opts.sparse_biom_to_dense_biom
dense_biom_to_sparse_biom = opts.dense_biom_to_sparse_biom
process_obs_metadata = opts.process_obs_metadata
if sum([biom_to_classic_table,
sparse_biom_to_dense_biom,
dense_biom_to_sparse_biom]) > 1:
parser.print_help()
option_parser.error("The --biom_to_classic_table, --sparse_biom_to_dense_biom, "
"and --dense_biom_to_sparse_biom options are mutually exclusive. Pass only one at a time.")
input_f = open(opts.input_fp,'U')
output_f = open(opts.output_fp,'w')
#dense = opts.biom_type == 'dense'
count_map_f = int
sample_mapping_fp = opts.sample_mapping_fp
obs_mapping_fp = opts.observation_mapping_fp
if sample_mapping_fp != None:
sample_mapping = parse_mapping(open(sample_mapping_fp,'U'))
else:
sample_mapping = None
if obs_mapping_fp != None:
obs_mapping = parse_mapping(open(obs_mapping_fp, 'U'))
else:
obs_mapping = None
# if the user does not specify a name for the output metadata column, set it to the
# same as the header key
header_key = opts.header_key
output_metadata_id = opts.output_metadata_id or header_key
if biom_to_classic_table:
try:
output_f.write(convert_biom_to_table(\
input_f, header_key, output_metadata_id))
except ValueError:
raise ValueError, "Input does not look like a .biom file. Did you accidentally specify -b?"
elif sparse_biom_to_dense_biom:
try:
table = parse_biom_table(input_f)
except ValueError:
raise ValueError, "Input does not look like a .biom file. Did you accidentally specify -b?"
conv_constructor = BIOM_TYPES[table._biom_type.lower()][1]
conv_table = table_factory(table._data, table.SampleIds,
table.ObservationIds, table.SampleMetadata,
table.ObservationMetadata, table.TableId,
constructor=conv_constructor)
output_f.write(conv_table.getBiomFormatJsonString(generatedby()))
elif dense_biom_to_sparse_biom:
try:
table = parse_biom_table(input_f)
except ValueError:
raise ValueError, "Input does not look like a .biom file. Did you accidentally specify -b?"
conv_constructor = BIOM_TYPES[table._biom_type.lower()][0]
conv_table = table_factory(table._data, table.SampleIds,
table.ObservationIds, table.SampleMetadata,
table.ObservationMetadata, table.TableId,
constructor=conv_constructor)
output_f.write(conv_table.getBiomFormatJsonString(generatedby()))
else:
if opts.biom_table_type is None:
parser.error('Must specify the BIOM table type: %s' % \
', '.join(BIOM_TYPES.keys()))
else:
biom_table_type = opts.biom_table_type.lower()
if biom_table_type not in BIOM_TYPES:
parser.error('Unknown BIOM table type, must be one of: %s' % \
', '.join(BIOM_TYPES.keys()))
if opts.biom_type is None or opts.biom_type not in ['dense', 'sparse']:
parser.error('Must specify the BIOM matrix type, ' + \
'either "dense" or "sparse"')
idx = 0 if opts.biom_type == 'sparse' else 1
constructor = BIOM_TYPES[biom_table_type][idx]
try:
output_f.write(convert_table_to_biom(input_f,sample_mapping,
obs_mapping, OBS_META_TYPES[process_obs_metadata], constructor))
except ValueError:
raise ValueError, "Input does not look like a classic table. Do you need to pass -b?"
input_f.close()
output_f.close()
def main():
opts,args = parser.parse_args()
if opts.input_fp is None:
parser.print_help()
parser.error('Must specify an input file!')
if opts.output_fp is None:
parser.print_help()
parser.error('Must specify an output file!')
## process header information, if provided
observation_header = opts.observation_header
sample_header = opts.sample_header
if opts.observation_header != None:
observation_header = observation_header.split(',')
if opts.sample_header != None:
sample_header = sample_header.split(',')
## define metadata processing functions, if any
process_fns = {}
sc_separated = opts.sc_separated
if sc_separated != None:
process_fns.update({}.fromkeys(sc_separated.split(','),
split_on_semicolons))
int_fields = opts.int_fields
if int_fields != None:
process_fns.update({}.fromkeys(int_fields.split(','),
int_))
float_fields = opts.float_fields
if float_fields != None:
process_fns.update({}.fromkeys(float_fields.split(','),
float_))
## parse mapping files
sample_mapping_fp = opts.sample_mapping_fp
obs_mapping_fp = opts.observation_mapping_fp
if sample_mapping_fp != None:
sample_mapping = parse_mapping(open(sample_mapping_fp,'U'),
process_fns=process_fns,
header=sample_header)
else:
sample_mapping = None
if obs_mapping_fp != None:
obs_mapping = parse_mapping(open(obs_mapping_fp, 'U'),
process_fns=process_fns,
header=observation_header)
else:
obs_mapping = None
if sample_mapping == None and obs_mapping == None:
parser.print_help()
parser.error('Must specify sample_mapping and/or obs_mapping.')
## parse the table and open the output file for writing
output_f = open(opts.output_fp,'w')
table = parse_biom_table(open(opts.input_fp,'U'))
## add metadata as necessary
if sample_mapping:
table.addSampleMetadata(sample_mapping)
if obs_mapping:
table.addObservationMetadata(obs_mapping)
## write the output file and close it
output_f.write(table.getBiomFormatJsonString(generatedby()))
output_f.close()