def test_make_otu_table_with_sample_metadata(self):
# Want to make sure that the order of the sample IDs in the OTU
# map and the order of the IDs in the mapping file do not matter
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
mapping_f = StringIO(MAPPING_FILE)
sample_ids = ['ABC', 'DEF', 'GHI', 'XYZ']
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
map_data, map_header, map_comments = parse_mapping_file(mapping_f)
sample_metadata = mapping_file_to_dict(map_data, map_header)
sample_md = [sample_metadata[sample_id] for sample_id in sample_ids]
obs = make_otu_table(otu_map_lines, sample_metadata=sample_metadata)
exp = Table(data, ['0', '1', 'x', 'z'], sample_ids,
sample_metadata=sample_md, input_is_dense=True)
self.assertEqual(obs, exp)
# Test with a mapping file that is missing a sample's metadata,
# make sure it raises the KeyError
mapping_f = StringIO(MAPPING_FILE_MISSING_SAMPLE)
map_data, map_header, map_comments = parse_mapping_file(mapping_f)
sample_metadata = mapping_file_to_dict(map_data, map_header)
with self.assertRaises(KeyError):
obs = make_otu_table(otu_map_lines,
sample_metadata=sample_metadata)
def test_make_otu_table_with_sample_metadata(self):
# Want to make sure that the order of the sample IDs in the OTU
# map and the order of the IDs in the mapping file do not matter
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
mapping_f = StringIO(MAPPING_FILE)
sample_ids = ['ABC', 'DEF', 'GHI', 'XYZ']
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
map_data, map_header, map_comments = parse_mapping_file(mapping_f)
sample_metadata = mapping_file_to_dict(map_data, map_header)
sample_md = [sample_metadata[sample_id] for sample_id in sample_ids]
obs = make_otu_table(otu_map_lines, sample_metadata=sample_metadata)
exp = Table(data, ['0', '1', 'x', 'z'],
sample_ids,
sample_metadata=sample_md,
input_is_dense=True)
self.assertEqual(obs, exp)
# Test with a mapping file that is missing a sample's metadata,
# make sure it raises the KeyError
mapping_f = StringIO(MAPPING_FILE_MISSING_SAMPLE)
map_data, map_header, map_comments = parse_mapping_file(mapping_f)
sample_metadata = mapping_file_to_dict(map_data, map_header)
with self.assertRaises(KeyError):
obs = make_otu_table(otu_map_lines,
sample_metadata=sample_metadata)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
outfile = open(opts.output_biom_fp, 'w')
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname,'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta','.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp,'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp,'U'))
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy,
ids_to_exclude)
outfile.write(biom_otu_table)
def _call_cleanup(self,
input_fp,
output_dir,
params,
job_prefix,
poll_directly,
suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params['observation_metadata_fp'] is not None:
observation_metadata = \
parse_observation_metadata(
open(params['observation_metadata_fp'], 'U'))
else:
observation_metadata = None
biom_fp = join(output_dir, 'observation_table.biom')
biom_table = make_otu_table(
open(join(output_dir, 'observation_map.txt'), 'U'),
observation_metadata)
write_biom_table(biom_table, biom_fp)
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass
def _call_cleanup(self,
input_fp,
output_dir,
params,
job_prefix,
poll_directly,
suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params['observation_metadata_fp'] is not None:
observation_metadata = \
parse_observation_metadata(
open(params['observation_metadata_fp'], 'U'))
else:
observation_metadata = None
biom_fp = join(output_dir, 'observation_table.biom')
biom_table = make_otu_table(
open(join(output_dir, 'observation_map.txt'), 'U'),
observation_metadata)
write_biom_table(biom_table, biom_fp)
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
mapping_data, mapping_header, mapping_comments = parse_mapping_file(open(opts.mapping_fp, 'U'))
sample_metadata = assemble_sample_metadata(mapping_data, mapping_header, mapping_comments)
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
with open(opts.mapping_fp, 'U') as map_f:
mapping_data, mapping_header, mapping_comments = \
parse_mapping_file(map_f)
sample_metadata = mapping_file_to_dict(mapping_data, mapping_header)
with open(opts.otu_map_fp, 'U') as otu_map_f:
biom_otu_table = make_otu_table(otu_map_f,
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def test_make_otu_table_taxonomy(self):
"""make_otu_table should work with taxonomy"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
taxonomy = {
'0': ['Bacteria', 'Firmicutes'],
'x': ['Bacteria', 'Bacteroidetes']
}
obs = make_otu_table(otu_map_lines, taxonomy)
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
obs_md = [{
'taxonomy': ['Bacteria', 'Firmicutes']
}, {
'taxonomy': ['None']
}, {
'taxonomy': ['Bacteria', 'Bacteroidetes']
}, {
'taxonomy': ['None']
}]
exp = Table(data, ['0', '1', 'x', 'z'], ['ABC', 'DEF', 'GHI', 'XYZ'],
observation_metadata=obs_md,
input_is_dense=True)
self.assertEqual(obs, exp)
def _generate_biom_output(self, observation_map_fp, output_biom_fp, observation_metadata_fp):
if observation_metadata_fp is not None:
observation_metadata = parse_taxonomy(open(observation_metadata_fp, "U"))
else:
observation_metadata = None
biom_table = make_otu_table(open(observation_map_fp, "U"), observation_metadata)
write_biom_table(biom_table, output_biom_fp)
def test_make_otu_table_no_taxonomy(self):
"""make_otu_table should work without tax (new-style OTU table)"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
obs = make_otu_table(otu_map_lines,constructor=DenseOTUTable)
exp = """{"rows": [{"id": "0", "metadata": null}, {"id": "1", "metadata": null}, {"id": "x", "metadata": null}, {"id": "z", "metadata": null}], "format": "Biological Observation Matrix 0.9dev", "data": [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]], "columns": [{"id": "ABC", "metadata": null}, {"id": "DEF", "metadata": null}, {"id": "GHI", "metadata": null}, {"id": "XYZ", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2532", "matrix_type": "dense", "shape": [4, 4], "format_url": "http://biom-format.org", "date": "2011-12-21T00:49:15.978315", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
self.assertEqual(parse_biom_table(obs.split('\n')), parse_biom_table(exp.split('\n')))
def test_make_otu_table_taxonomy(self):
"""make_otu_table should work with taxonomy"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
# Single taxonomic assignment.
taxonomy = {'0':'Bacteria;Firmicutes', 'x':'Bacteria;Bacteroidetes'}
obs = make_otu_table(otu_map_lines, taxonomy,constructor=DenseOTUTable)
exp = """{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Firmicutes"]}}, {"id": "1", "metadata": {"taxonomy": ["None"]}}, {"id": "x", "metadata": {"taxonomy": ["Bacteria", "Bacteroidetes"]}}, {"id": "z", "metadata": {"taxonomy": ["None"]}}], "format": "Biological Observation Matrix 0.9dev", "data": [[1.0, 1.0, 0.0, 0.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 3.0, 0.0], [0.0, 1.0, 0.0, 1.0]], "columns": [{"id": "ABC", "metadata": null}, {"id": "DEF", "metadata": null}, {"id": "GHI", "metadata": null}, {"id": "XYZ", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2532", "matrix_type": "dense", "shape": [4, 4], "format_url": "http://biom-format.org", "date": "2011-12-21T00:19:30.961477", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
self.assertEqual(parse_biom_table(obs.split('\n')), parse_biom_table(exp.split('\n')))
# Multiple taxonomic assignments.
taxonomy = {'0':['Bacteria;Firmicutes'], 'x':['Bacteria;Bacteroidetes', 'Bacteria;Acidobacteria']}
obs = make_otu_table(otu_map_lines, taxonomy,constructor=DenseOTUTable)
exp = """{"rows": [{"id": "0", "metadata": {"taxonomy": [["Bacteria", "Firmicutes"]]}}, {"id": "1", "metadata": {"taxonomy": ["None"]}}, {"id": "x", "metadata": {"taxonomy": [["Bacteria", "Bacteroidetes"], ["Bacteria", "Acidobacteria"]]}}, {"id": "z", "metadata": {"taxonomy": ["None"]}}], "format": "Biological Observation Matrix 0.9dev", "data": [[1.0, 1.0, 0.0, 0.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 3.0, 0.0], [0.0, 1.0, 0.0, 1.0]], "columns": [{"id": "ABC", "metadata": null}, {"id": "DEF", "metadata": null}, {"id": "GHI", "metadata": null}, {"id": "XYZ", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2532", "matrix_type": "dense", "shape": [4, 4], "format_url": "http://biom-format.org", "date": "2011-12-21T00:19:30.961477", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
self.assertEqual(parse_biom_table(obs.split('\n')), parse_biom_table(exp.split('\n')))
def _generate_biom_output(self, observation_map_fp, output_biom_fp, observation_metadata_fp):
if observation_metadata_fp is not None:
observation_metadata = parse_taxonomy(open(observation_metadata_fp, "U"))
else:
observation_metadata = None
biom_table_f = open(output_biom_fp, "w")
biom_table_f.write(make_otu_table(open(observation_map_fp, "U"), observation_metadata))
biom_table_f.close()
def test_make_otu_table_no_taxonomy(self):
"""make_otu_table should work without tax (new-style OTU table)"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
obs = make_otu_table(otu_map_lines, constructor=DenseOTUTable)
exp = """{"rows": [{"id": "0", "metadata": null}, {"id": "1", "metadata": null}, {"id": "x", "metadata": null}, {"id": "z", "metadata": null}], "format": "Biological Observation Matrix 0.9dev", "data": [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]], "columns": [{"id": "ABC", "metadata": null}, {"id": "DEF", "metadata": null}, {"id": "GHI", "metadata": null}, {"id": "XYZ", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2532", "matrix_type": "dense", "shape": [4, 4], "format_url": "http://biom-format.org", "date": "2011-12-21T00:49:15.978315", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
self.assertEqual(parse_biom_table(obs.split('\n')),
parse_biom_table(exp.split('\n')))
def _generate_biom_output(self, observation_map_fp, output_biom_fp,
observation_metadata_fp):
if observation_metadata_fp is not None:
observation_metadata = \
parse_taxonomy(open(observation_metadata_fp, 'U'))
else:
observation_metadata = None
biom_table = make_otu_table(open(observation_map_fp, 'U'),
observation_metadata)
write_biom_table(biom_table, output_biom_fp)
def test_make_otu_table_taxonomy(self):
"""make_otu_table should work with taxonomy"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
taxonomy = {'0': 'Bacteria;Firmicutes', 'x': 'Bacteria;Bacteroidetes'}
obs = make_otu_table(otu_map_lines,
taxonomy,
constructor=DenseOTUTable)
exp = """{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Firmicutes"]}}, {"id": "1", "metadata": {"taxonomy": ["None"]}}, {"id": "x", "metadata": {"taxonomy": ["Bacteria", "Bacteroidetes"]}}, {"id": "z", "metadata": {"taxonomy": ["None"]}}], "format": "Biological Observation Matrix 0.9dev", "data": [[1.0, 1.0, 0.0, 0.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 3.0, 0.0], [0.0, 1.0, 0.0, 1.0]], "columns": [{"id": "ABC", "metadata": null}, {"id": "DEF", "metadata": null}, {"id": "GHI", "metadata": null}, {"id": "XYZ", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2532", "matrix_type": "dense", "shape": [4, 4], "format_url": "http://biom-format.org", "date": "2011-12-21T00:19:30.961477", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
self.assertEqual(parse_biom_table(obs.split('\n')),
parse_biom_table(exp.split('\n')))
def test_make_otu_table_no_taxonomy(self):
"""make_otu_table should work without tax (new-style OTU table)"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
obs = make_otu_table(otu_map_lines)
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
exp = Table(data, ['0', '1', 'x', 'z'], ['ABC', 'DEF', 'GHI', 'XYZ'],
input_is_dense=True)
self.assertEqual(obs, exp)
def test_make_otu_table_no_taxonomy(self):
"""make_otu_table should work without tax (new-style OTU table)"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
obs = make_otu_table(otu_map_lines)
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
exp = Table(data, ['0', '1', 'x', 'z'], ['ABC', 'DEF', 'GHI', 'XYZ'],
input_is_dense=True)
self.assertEqual(obs, exp)
def _generate_biom_output(self, observation_map_fp, output_biom_fp,
observation_metadata_fp):
if observation_metadata_fp != None:
observation_metadata = \
parse_taxonomy(open(observation_metadata_fp,'U'))
else:
observation_metadata = None
biom_table_f = open(output_biom_fp, 'w')
biom_table_f.write(
make_otu_table(open(observation_map_fp, 'U'),
observation_metadata))
biom_table_f.close()
def _generate_biom_output(self,
observation_map_fp,
output_biom_fp,
observation_metadata_fp):
if observation_metadata_fp != None:
observation_metadata = \
parse_taxonomy(open(observation_metadata_fp,'U'),
parse_all_fields=True)
else:
observation_metadata = None
biom_table_f = open(output_biom_fp,'w')
biom_table_f.write(make_otu_table(open(observation_map_fp,'U'),
observation_metadata))
biom_table_f.close()
def test_make_otu_table_no_taxonomy(self):
"""make_otu_table should work without tax (new-style OTU table)"""
otu_to_seqid ={ '0':['ABC_0','DEF_1'],
'1':['ABC_1'],
'x':['GHI_2', 'GHI_3','GHI_77'],
'z':['DEF_3','XYZ_1']
}
obs = make_otu_table(otu_to_seqid, legacy=False)
exp = """# QIIME v%s OTU table
OTU ID\tABC\tDEF\tGHI\tXYZ
0\t1\t1\t0\t0
1\t1\t0\t0\t0
x\t0\t0\t3\t0
z\t0\t1\t0\t1""" % __version__
self.assertEqual(obs, exp)
def test_make_otu_table_taxonomy(self):
"""make_otu_table should work wit tax (new-style OTU table)"""
otu_to_seqid ={ '0':['ABC_0','DEF_1'],
'1':['ABC_1'],
'x':['GHI_2', 'GHI_3','GHI_77'],
'z':['DEF_3','XYZ_1']
}
taxonomy = {'0':'Bacteria;Firmicutes', 'x':'Bacteria;Bacteroidetes'}
obs = make_otu_table(otu_to_seqid, taxonomy, legacy=False)
exp = """# QIIME v%s OTU table
OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes
1\t1\t0\t0\t0\tNone
x\t0\t0\t3\t0\tBacteria;Bacteroidetes
z\t0\t1\t0\t1\tNone""" % __version__
self.assertEqual(obs, exp)
def _call_cleanup(self, input_fp, output_dir, params, job_prefix, poll_directly, suppress_submit_jobs):
""" Called as the last step in __call__.
"""
if poll_directly:
if params["observation_metadata_fp"] != None:
observation_metadata = parse_observation_metadata(open(params["observation_metadata_fp"], "U"))
else:
observation_metadata = None
biom_fp = join(output_dir, "observation_table.biom")
biom_f = open(biom_fp, "w")
biom_f.write(make_otu_table(open(join(output_dir, "observation_map.txt"), "U"), observation_metadata))
biom_f.close()
else:
# can't construct the final biom file if not polling
# directly as the final observation map won't have been created yet
pass
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
if not opts.counts_fname:
seq_counts = None
else:
seq_counts = {}
with open(opts.counts_fname, 'U') as infile:
for line in infile:
(key, val) = line.split()
seq_counts[key] = val
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
with open(opts.mapping_fp, 'U') as map_f:
mapping_data, mapping_header, mapping_comments = \
parse_mapping_file(map_f)
sample_metadata = mapping_file_to_dict(mapping_data,
mapping_header)
with open(opts.otu_map_fp, 'U') as otu_map_f:
biom_otu_table = make_otu_table(otu_map_f,
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata,seq_counts=seq_counts)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def test_make_otu_table_taxonomy(self):
"""make_otu_table should work with taxonomy"""
otu_map_lines = """0 ABC_0 DEF_1
1 ABC_1
x GHI_2 GHI_3 GHI_77
z DEF_3 XYZ_1""".split('\n')
taxonomy = {'0': ['Bacteria', 'Firmicutes'],
'x': ['Bacteria', 'Bacteroidetes']}
obs = make_otu_table(otu_map_lines, taxonomy)
data = [[1, 1, 0, 0], [1, 0, 0, 0], [0, 0, 3, 0], [0, 1, 0, 1]]
obs_md = [{'taxonomy': ['Bacteria', 'Firmicutes']},
{'taxonomy': ['None']},
{'taxonomy': ['Bacteria', 'Bacteroidetes']},
{'taxonomy': ['None']}]
exp = Table(data, ['0', '1', 'x', 'z'], ['ABC', 'DEF', 'GHI', 'XYZ'],
observation_metadata=obs_md, input_is_dense=True)
self.assertEqual(obs, exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if opts.output_fp:
outfile = open(opts.output_fp, 'w')
else:
outfile = stdout
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname,'U')
otu_to_taxonomy = parse_taxonomy(infile)
otu_to_seqid = fields_to_dict(open(opts.otu_map_fp, 'U'))
if exclude_otus_fp:
otu_to_seqid = remove_otus(otu_to_seqid,open(exclude_otus_fp,'U'))
outfile.write(make_otu_table(otu_to_seqid, otu_to_taxonomy))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
outfile = open(opts.output_biom_fp, 'w')
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy, ids_to_exclude)
outfile.write(biom_otu_table)
