def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dirs = opts.input_dirs.split(',')
assignment_methods = opts.assignment_methods.split(',')
confidences = opts.confidences
if confidences is not None:
confidences = map(float, opts.confidences.split(','))
e_values = opts.e_values
if e_values is not None:
e_values = map(float, opts.e_values.split(','))
if opts.print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if opts.verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
assign_taxonomy_multiple_times(input_dirs, opts.output_dir,
assignment_methods, opts.reference_seqs_fp, opts.input_fasta_filename,
opts.clean_otu_table_filename,
id_to_taxonomy_fp=opts.id_to_taxonomy_fp,
confidences=confidences, e_values=e_values,
read_1_seqs_fp=opts.read_1_seqs_fp,
read_2_seqs_fp=opts.read_2_seqs_fp,
rdp_max_memory=opts.rdp_max_memory,
command_handler=command_handler,
status_update_callback=status_update_callback, force=opts.force)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dirs = opts.input_dirs.split(',')
assignment_methods = opts.assignment_methods.split(',')
confidences = split_input_str(opts.confidences)
e_values = split_input_str(opts.e_values)
rtax_modes = split_input_str(opts.rtax_modes, map_fn=str)
uclust_min_consensus_fractions = \
split_input_str(opts.uclust_min_consensus_fractions)
uclust_similarities = split_input_str(opts.uclust_similarities)
uclust_max_accepts = split_input_str(opts.uclust_max_accepts, map_fn=int)
rtax_read_id_regexes = split_input_str(opts.rtax_read_id_regexes,
map_fn=str)
rtax_amplicon_id_regexes = split_input_str(opts.rtax_amplicon_id_regexes,
map_fn=str)
rtax_header_id_regexes = split_input_str(opts.rtax_header_id_regexes,
map_fn=str)
if opts.print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if opts.verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
assign_taxonomy_multiple_times(input_dirs, opts.output_dir,
assignment_methods, opts.reference_seqs_fp,
opts.id_to_taxonomy_fp, confidences=confidences,
e_values=e_values, rtax_modes=rtax_modes,
uclust_min_consensus_fractions=uclust_min_consensus_fractions,
uclust_similarities=uclust_similarities,
uclust_max_accepts=uclust_max_accepts,
input_fasta_filename=opts.input_fasta_filename,
clean_otu_table_filename=opts.clean_otu_table_filename,
read_1_seqs_filename=opts.read_1_seqs_filename,
read_2_seqs_filename=opts.read_2_seqs_filename,
rtax_read_id_regexes=rtax_read_id_regexes,
rtax_amplicon_id_regexes=rtax_amplicon_id_regexes,
rtax_header_id_regexes=rtax_header_id_regexes,
rdp_max_memory=opts.rdp_max_memory,
command_handler=command_handler,
status_update_callback=status_update_callback, force=opts.force)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dirs = opts.input_dirs.split(',')
assignment_methods = opts.assignment_methods.split(',')
confidences = opts.confidences
if confidences is not None:
confidences = map(float, opts.confidences.split(','))
e_values = opts.e_values
if e_values is not None:
e_values = map(float, opts.e_values.split(','))
if opts.print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if opts.verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
assign_taxonomy_multiple_times(
input_dirs,
opts.output_dir,
assignment_methods,
opts.reference_seqs_fp,
opts.input_fasta_filename,
opts.clean_otu_table_filename,
id_to_taxonomy_fp=opts.id_to_taxonomy_fp,
confidences=confidences,
e_values=e_values,
read_1_seqs_fp=opts.read_1_seqs_fp,
read_2_seqs_fp=opts.read_2_seqs_fp,
rdp_max_memory=opts.rdp_max_memory,
command_handler=command_handler,
status_update_callback=status_update_callback,
force=opts.force)
def test_assign_taxonomy_multiple_times_invalid_input_uclust(self):
"""Test that errors are thrown using invalid input for uclust."""
out_dir = self.output_dir
# Missing uclust consensus parameters.
with self.assertRaises(WorkflowError):
assign_taxonomy_multiple_times([out_dir, out_dir], out_dir,
['uclust', 'uclust'], '/foo/ref_seqs.fasta',
'/foo/tax.txt', rtax_modes=['single'], force=True)
# Missing uclust similarity parameters.
with self.assertRaises(WorkflowError):
assign_taxonomy_multiple_times([out_dir, out_dir], out_dir,
['uclust', 'uclust'], '/foo/ref_seqs.fasta',
'/foo/tax.txt', uclust_min_consensus_fractions=[0.51],
force=True)
# Missing uclust max accepts parameters.
with self.assertRaises(WorkflowError):
assign_taxonomy_multiple_times([out_dir, out_dir], out_dir,
['uclust', 'uclust'], '/foo/ref_seqs.fasta',
'/foo/tax.txt', uclust_min_consensus_fractions=[0.51],
uclust_similarities=[0.97], force=True)