def test_get_reference_tree(self):
fp = get_reference_tree()
self.assertIn(os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'),
fp)
self.assertTrue(os.path.isfile(fp))
self.assertTrue(os.path.isabs(fp))
with open(fp, 'rb') as f:
md5 = safe_md5(f).hexdigest()
self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')
def test_get_reference_tree(self):
fp = get_reference_tree()
self.assertIn(
os.path.join('gg_13_8_otus', 'trees', '97_otus.tree'), fp)
self.assertTrue(os.path.isfile(fp))
self.assertTrue(os.path.isabs(fp))
with open(fp, 'rb') as f:
md5 = safe_md5(f).hexdigest()
self.assertEqual(md5, 'b7e76593bce82913af1cfb06edf15732')
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
input_fp = opts.input_fp
reference_fp = opts.reference_fp
taxonomy_fp = opts.taxonomy_fp
output_dir = opts.output_dir
verbose = opts.verbose
print_only = opts.print_only
assign_taxonomy = opts.assign_taxonomy
if opts.suppress_taxonomy_assignment:
assign_taxonomy = False
taxonomy_fp = None
parallel = opts.parallel
# No longer checking that jobs_to_start > 2, but
# commenting as we may change our minds about this.
# if parallel: raise_error_on_parallel_unavailable()
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp, 'U')
except IOError:
raise IOError("Can't open parameters file (%s). Does it exist? Do you have read access?"
% opts.parameter_fp)
params = parse_qiime_parameters(parameter_f)
parameter_f.close()
else:
params = parse_qiime_parameters([])
# empty list returns empty defaultdict for now
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params,
jobs_to_start,
default_jobs_to_start,
parallel,
option_parser)
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
option_parser.error("Output directory already exists. Please choose"
" a different directory, or force overwrite with -f.")
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_pick_closed_reference_otus(
input_fp,
reference_fp,
output_dir,
taxonomy_fp,
assign_taxonomy=assign_taxonomy,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
status_update_callback=status_update_callback)
if get_reference_sequences() == reference_fp:
reference_tree_fp = get_reference_tree()
fn = basename(reference_tree_fp)
copyfile(reference_tree_fp, join(output_dir, fn))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
input_fp = opts.input_fp
reference_fp = opts.reference_fp
taxonomy_fp = opts.taxonomy_fp
output_dir = opts.output_dir
verbose = opts.verbose
print_only = opts.print_only
assign_taxonomy = opts.assign_taxonomy
if opts.suppress_taxonomy_assignment:
assign_taxonomy = False
taxonomy_fp = None
parallel = opts.parallel
# No longer checking that jobs_to_start > 2, but
# commenting as we may change our minds about this.
# if parallel: raise_error_on_parallel_unavailable()
if opts.parameter_fp:
try:
parameter_f = open(opts.parameter_fp, 'U')
except IOError:
raise IOError(
"Can't open parameters file (%s). Does it exist? Do you have read access?"
% opts.parameter_fp)
params = parse_qiime_parameters(parameter_f)
parameter_f.close()
else:
params = parse_qiime_parameters([])
# empty list returns empty defaultdict for now
jobs_to_start = opts.jobs_to_start
default_jobs_to_start = qiime_config['jobs_to_start']
validate_and_set_jobs_to_start(params, jobs_to_start,
default_jobs_to_start, parallel,
option_parser)
if print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
try:
makedirs(output_dir)
except OSError:
if opts.force:
pass
else:
option_parser.error(
"Output directory already exists. Please choose"
" a different directory, or force overwrite with -f.")
if verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
run_pick_closed_reference_otus(
input_fp,
reference_fp,
output_dir,
taxonomy_fp,
assign_taxonomy=assign_taxonomy,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
status_update_callback=status_update_callback)
if get_reference_sequences() == reference_fp:
reference_tree_fp = get_reference_tree()
fn = basename(reference_tree_fp)
copyfile(reference_tree_fp, join(output_dir, fn))
