def test_split_mapping_file_on_field(self):
""" split_mapping_file_on_field functions as expected with valid input
"""
actual = sorted(
split_mapping_file_on_field(self.mapping_f1, 'Treatment'))
self.mapping_exp.sort()
self.assertEqual(actual, self.mapping_exp)
def test_split_mapping_file_on_field(self):
""" split_mapping_file_on_field functions as expected with valid input
"""
actual = list(split_mapping_file_on_field(self.mapping_f1,'Treatment'))
actual.sort()
self.mapping_exp.sort()
self.assertEqual(actual,self.mapping_exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
mapping_field = opts.mapping_field
output_dir = opts.output_dir
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
create_dir(output_dir)
# split mapping file
mapping_f = open(mapping_fp, 'U')
for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field):
mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str)
open(mapping_output_fp, 'w').write(sub_mapping_s)
# split otu table
otu_table_base_name = splitext(split(otu_table_fp)[1])[0]
mapping_f = open(mapping_fp, 'U')
otu_table = load_table(otu_table_fp)
try:
for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata(
otu_table,
mapping_f,
mapping_field):
otu_table_output_fp = join(output_dir, '%s_%s.biom' % (
otu_table_base_name, fp_str))
write_biom_table(sub_otu_table_s, otu_table_output_fp)
except OTUTableSplitError as e:
option_parser.error(e)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
mapping_field = opts.mapping_field
output_dir = opts.output_dir
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
create_dir(output_dir)
# split mapping file
mapping_f = open(mapping_fp, 'U')
for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field):
mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str)
open(mapping_output_fp, 'w').write(sub_mapping_s)
# split otu table
otu_table_base_name = splitext(split(otu_table_fp)[1])[0]
mapping_f = open(mapping_fp, 'U')
otu_table_f = open(otu_table_fp, 'U')
for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata(
otu_table_f,
mapping_f,
mapping_field):
otu_table_output_fp = join(
output_dir, '%s_%s.biom' %
(otu_table_base_name, fp_str))
open(otu_table_output_fp, 'w').write(sub_otu_table_s)
