def test_natsort_case_insensitive(self):
"""natsort should perform numeric comparisons on strings and is
_not_ case-sensitive"""
# string with alpha and numerics sort correctly
s = [
'sample1',
'sample2',
'sample11',
'sample12',
'SAmple1',
'Sample2']
# expected values
exp_natsort = ['SAmple1', 'Sample2', 'sample1', 'sample2', 'sample11',
'sample12']
exp_natsort_case_insensitive = ['sample1', 'SAmple1', 'sample2',
'Sample2', 'sample11', 'sample12']
# test natsort
self.assertEqual(natsort(s), exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort_case_insensitive(s),
exp_natsort_case_insensitive)
s.reverse()
# test natsort
self.assertEqual(natsort(s), exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort(list('cbaA321')), list('123Aabc'))
# strings with alpha only sort correctly
self.assertEqual(natsort_case_insensitive(list('cdBa')), list('aBcd'))
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive(['11', '2', '1', '0']),
['0', '1', '2', '11'])
# strings of floats sort correctly
self.assertEqual(natsort_case_insensitive(['1.11', '1.12', '1.00',
'0.009']), ['0.009', '1.00',
'1.11', '1.12'])
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive([('11', 'A'), ('2', 'B'),
('1', 'C'), ('0', 'D')]),
[('0', 'D'), ('1', 'C'),
('2', 'B'), ('11', 'A')])
def test_natsort_case_insensitive(self):
"""natsort should perform numeric comparisons on strings and is
_not_ case-sensitive"""
# string with alpha and numerics sort correctly
s = [
'sample1',
'sample2',
'sample11',
'sample12',
'SAmple1',
'Sample2']
# expected values
exp_natsort = ['SAmple1', 'Sample2', 'sample1', 'sample2', 'sample11',
'sample12']
exp_natsort_case_insensitive = ['sample1', 'SAmple1', 'sample2',
'Sample2', 'sample11', 'sample12']
# test natsort
self.assertEqual(natsort(s), exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort_case_insensitive(s),
exp_natsort_case_insensitive)
s.reverse()
# test natsort
self.assertEqual(natsort(s), exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort(list('cbaA321')), list('123Aabc'))
# strings with alpha only sort correctly
self.assertEqual(natsort_case_insensitive(list('cdBa')), list('aBcd'))
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive(['11', '2', '1', '0']),
['0', '1', '2', '11'])
# strings of floats sort correctly
self.assertEqual(natsort_case_insensitive(['1.11', '1.12', '1.00',
'0.009']), ['0.009', '1.00',
'1.11', '1.12'])
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive([('11', 'A'), ('2', 'B'),
('1', 'C'), ('0', 'D')]),
[('0', 'D'), ('1', 'C'),
('2', 'B'), ('11', 'A')])
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_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 = 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)
