/usr/bin/convert_biom is in python-biom-format 1.1.2-1.
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# File created on 20 Dec 2011
from __future__ import division
from optparse import make_option, OptionParser, OptionGroup
from biom.table import SparseOTUTable, DenseOTUTable, SparsePathwayTable, \
DensePathwayTable, SparseFunctionTable, DenseFunctionTable, \
SparseOrthologTable, DenseOrthologTable, SparseGeneTable, \
DenseGeneTable, SparseMetaboliteTable, DenseMetaboliteTable,\
SparseTaxonTable, DenseTaxonTable, table_factory
from biom.parse import parse_biom_table, parse_mapping, convert_biom_to_table, \
convert_table_to_biom, generatedby
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2012, The BIOM-Format project"
__credits__ = ["Greg Caporaso", "Daniel McDonald",
"Jose Carlos Clemente Litran", "Jai Ram Rideout"]
__license__ = "GPL"
__url__ = "http://biom-format.org"
__version__ = "1.1.2"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
BIOM_TYPES = {'otu table':[SparseOTUTable, DenseOTUTable],
'pathway table':[SparsePathwayTable, DensePathwayTable],
'function table':[SparseFunctionTable, DenseFunctionTable],
'ortholog table':[SparseOrthologTable, DenseOrthologTable],
'gene table':[SparseGeneTable, DenseGeneTable],
'metabolite table':[SparseMetaboliteTable, DenseMetaboliteTable],
'taxon table':[SparseTaxonTable, DenseTaxonTable]}
OBS_META_TYPES = {'sc_separated': lambda x: [e.strip() for e in x.split(';')],
'naive': lambda x: x
}
OBS_META_TYPES['taxonomy'] = OBS_META_TYPES['sc_separated']
usage = "usage: Detailed usage examples can be found here: http://biom-format.org/documentation/biom_conversion.html"
desc = "Script to convert biom formatted files."
parser = OptionParser(usage=usage, description=desc, version=__version__)
parser.set_defaults(verbose=True)
req_group = OptionGroup(parser, 'Required Options')
req_options = [make_option('-i','--input_fp',type="string",
help='the input filepath'),
make_option('-o','--output_fp',type="string",
help='the output filepath')]
req_group.add_options(req_options)
parser.add_option_group(req_group)
opt_group = OptionGroup(parser, 'Optional Options')
opt_options = [make_option('-t','--biom_type',type='choice',
choices=['sparse','dense'],default='sparse',
help="Type of biom file to write (dense or sparse) when "
"passed a classic table [default: %default]"),
make_option('-b','--biom_to_classic_table',
action='store_true', help="Convert biom file to classic "
"table file [default: convert "
"classic table file to biom file]",default=False),
make_option('--sparse_biom_to_dense_biom',action='store_true',
help="Convert sparse biom file to a dense biom file "
"[default: convert "
"classic table file to biom file]",default=False),
make_option('--dense_biom_to_sparse_biom',action='store_true',
help="Convert dense biom file to a sparse biom file "
"[default: convert "
"classic table file to biom file]",default=False),
make_option('-m','--sample_mapping_fp',type="string",
help='The mapping filepath (will add sample metadata to '
'biom file, if provided) [default: %default]'),
make_option('--observation_mapping_fp',type="string",
help='The mapping filepath (will add observation metadata '
'to biom file, if provided) [default: %default]'),
make_option('--header_key',type="string",default=None,
help='Pull this key from observation metadata within a '
'biom file when writing a classic table [default: no '
'observation metadata will be written]'),
make_option('--output_metadata_id',type="string",default=None,
help='Name for the observation metadata column when '
'writing a biom file as a classic table [default: same '
'name as in biom-formatted table]'),
make_option('--process_obs_metadata',type="choice",
choices=OBS_META_TYPES.keys(), default='naive',
help='Process metadata associated with observations when '
'converting from a classic table. Must be one of: ' +
', '.join(OBS_META_TYPES.keys()) + ' [default: %default]'),
make_option('--biom_table_type',type="string",default=None,
help='The biom table type to get converted into. Required '
'when converting a classic table file to biom file. Must '
'be one of: %s' % ', '.join(BIOM_TYPES.keys()))]
opt_group.add_options(opt_options)
parser.add_option_group(opt_group)
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()
if __name__ == "__main__":
main()
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