def test_sequences_for_query_string(self):
"""Check correct parsing when input is a string"""
out_tax_dict = sequences_for_query(self.taxonomy_lines, 'Beggiatoa')
self.assertEquals(out_tax_dict, {'NZ_ABBZ01000843|640963011':
'VibrioBeggiatoa sp. PS', 'NZ_ABBZ01000613|640963011':
'VibrioBeggiatoa sp. PS', 'NZ_ABBZ01002042|640963011':
'VibrioBeggiatoa sp. PS', 'NZ_ABBY01000503|640963012':
'VibrioBeggiatoa sp. SS', 'NZ_ABBZ01000140|640963011':
'VibrioBeggiatoa sp. PS', 'NZ_ABBY01000221|640963012':
'VibrioBeggiatoa sp. SS', 'NZ_ABBZ01006278|640963011':
'VibrioBeggiatoa sp. PS', 'NZ_ABBZ01005870|640963011':
'VibrioBeggiatoa sp. PS'})
out_tax_dict = sequences_for_query(self.taxonomy_lines, 'Rumba')
self.assertEquals(out_tax_dict, {})
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
taxonomy_fp = opts.taxonomy_fp
fasta_fp = opts.fasta_fp
query = opts.query
output_fp = opts.output_fp
# query the taxonomy file for the required sequence identifiers
try:
taxonomy_dict = sequences_for_query(open(taxonomy_fp, 'U'), query)
except (PlatypusValueError, PlatypusParseError), e:
option_parser.error(e.message)
