def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_data = parse_biom_table(open(opts.input_otu_table, 'U'))
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
result = sort_otu_table(otu_table_data, sorted_sample_ids)
else:
result = sort_otu_table(
otu_table_data, natsort_case_insensitive(otu_table_data.SampleIds))
# format and write the otu table
result_str = format_biom_table(result)
of = open(opts.output_fp, 'w')
of.write(result_str)
of.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_data = parse_otu_table(open(opts.input_otu_table,'U'))
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp,'U'))
result = sort_otu_table_by_mapping_field(otu_table_data,
mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp,'U'))
result = sort_otu_table(otu_table_data,
sorted_sample_ids)
else:
parser.error("must provide either --sort_field and --mapping_fp OR --sorted_sample_ids_fp")
# format and write the otu table
result_str = format_otu_table(result[0],result[1],result[2],result[3])
of = open(opts.output_fp,'w')
of.write(result_str)
of.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_data = parse_biom_table(open(opts.input_otu_table,'U'))
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp,'U'))
result = sort_otu_table_by_mapping_field(otu_table_data,
mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp,'U'))
result = sort_otu_table(otu_table_data,
sorted_sample_ids)
else:
result = sort_otu_table(otu_table_data,
natsort_case_insensitive(otu_table_data.SampleIds))
# format and write the otu table
result_str = format_biom_table(result)
of = open(opts.output_fp,'w')
of.write(result_str)
of.close()
def test_sort_otu_table_by_mapping_field_some_values_same(self):
""" sort_otu_table_by_mapping_field fns when all values are the same"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Name")
expected = parse_biom_table_str(self.name_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_by_mapping_field_some_values_differ(self):
""" sort_otu_table fns when some values differ"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Nothing")
expected = parse_biom_table_str(self.nothing_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_by_mapping_field_all_values_differ(self):
""" sort_otu_table_by_mapping_field fns when all values differ"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Age")
expected = parse_biom_table_str(self.age_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_by_mapping_field_some_values_same(self):
""" sort_otu_table_by_mapping_field fns when all values are the same"""
actual = sort_otu_table_by_mapping_field(parse_otu_table(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Name")
expected = parse_otu_table(self.name_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
def test_sort_otu_table_by_mapping_field_some_values_differ(self):
""" sort_otu_table fns when some values differ"""
actual = sort_otu_table_by_mapping_field(parse_otu_table(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Nothing")
expected = parse_otu_table(self.nothing_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_data = load_table(opts.input_otu_table)
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
result = sort_otu_table(otu_table_data, sorted_sample_ids)
else:
result = sort_otu_table(otu_table_data,
natsort_case_insensitive(otu_table_data.ids()))
write_biom_table(result, opts.output_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_data = load_table(opts.input_otu_table)
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp, 'U'))
result = sort_otu_table_by_mapping_field(otu_table_data, mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp, 'U'))
result = sort_otu_table(otu_table_data,
sorted_sample_ids)
else:
result = sort_otu_table(otu_table_data,
natsort_case_insensitive(otu_table_data.ids()))
write_biom_table(result, opts.output_fp)
