def test_add_counts_to_mapping(self):
"""NumIndividuals is added to the mapping file"""
# Get the output filepath
out_fp = get_tmp_filename(tmp_dir=self.tmp_dir, suffix='.txt')
# Add the output filepath to clean variable
self._paths_to_clean_up = [out_fp]
# Perform the test
add_counts_to_mapping(self.biom_table, self.mapping, False, out_fp)
f = open(out_fp, 'U')
obs = f.readlines()
f.close()
self.assertEqual(obs, exp_mapping_file_seqs.splitlines(True))
# Get the output filepath
out_fp = get_tmp_filename(tmp_dir=self.tmp_dir, suffix='.txt')
# Add the output filepath to clean variable
self._paths_to_clean_up.append(out_fp)
# Perform the test
add_counts_to_mapping(self.biom_table, self.mapping, True, out_fp)
f = open(out_fp, 'U')
obs = f.readlines()
f.close()
self.assertEqual(obs, exp_mapping_file_otu.splitlines(True))
'--input_fp',
type="existing_filepath",
help='Biom table filepath'),
make_option('-m',
'--mapping_fp',
type="existing_filepath",
help='Mapping file filepath'),
make_option('-o',
'--output_fp',
type="new_filepath",
help='Output mapping filepath')
]
script_info['optional_options'] = [
make_option(
'--otu_counts',
action='store_true',
default=False,
help='Counts are presented as number of observed OTUs per sample, ' +
'rather than counts of sequences per sample [default: %default]')
]
script_info['version'] = __version__
if __name__ == '__main__':
option_parser, opts, args = parse_command_line_parameters(**script_info)
biom_fp = opts.input_fp
mapping_fp = opts.mapping_fp
output_fp = opts.output_fp
otu_counts = opts.otu_counts
add_counts_to_mapping(open(biom_fp, 'U'), open(mapping_fp, 'U'),
otu_counts, output_fp)
"%prog -i otu_table.biom -m mapping_file.txt -o mapping_w_counts.txt"),
("Example", "Count the number of OTUs per sample present in " + \
"'otu_table.biom' and add this counts to 'mapping_file.txt'",
"%prog -i otu_table.biom -m mapping_file.txt --otu_counts " + \
"-o mapping_w_counts.txt")
]
script_info['output_description'] = "The mapping file with the counts added"
script_info['required_options'] = [
make_option('-i', '--input_fp', type="existing_filepath",
help='Biom table filepath'),
make_option('-m', '--mapping_fp', type="existing_filepath",
help='Mapping file filepath'),
make_option('-o', '--output_fp', type="new_filepath",
help='Output mapping filepath')
]
script_info['optional_options'] = [
make_option('--otu_counts', action='store_true', default=False,
help='Counts are presented as number of observed OTUs per sample, ' +
'rather than counts of sequences per sample [default: %default]')
]
script_info['version'] = __version__
if __name__ == '__main__':
option_parser, opts, args = parse_command_line_parameters(**script_info)
biom_fp = opts.input_fp
mapping_fp = opts.mapping_fp
output_fp = opts.output_fp
otu_counts = opts.otu_counts
add_counts_to_mapping(open(biom_fp, 'U'), open(mapping_fp, 'U'), otu_counts,
output_fp)
