def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create the output dir if it doesn't already exist.
try:
if not path.exists(opts.output_dir):
create_dir(opts.output_dir)
except:
option_parser.error("Could not create or access output directory "
"specified with the -o option.")
sample_id_map = None
if opts.sample_id_map_fp:
sample_id_map = dict([(k, v[0]) for k, v in fields_to_dict(
open(opts.sample_id_map_fp, "U")).items()])
input_dm_fps = opts.input_dms
distmats = [parse_distmat(open(dm_fp, 'U')) for dm_fp in input_dm_fps]
if opts.method == 'mantel':
output_f = open(path.join(opts.output_dir, 'mantel_results.txt'), 'w')
output_f.write(
run_mantel_test('mantel',
input_dm_fps,
distmats,
opts.num_permutations,
opts.tail_type,
comment_mantel_pmantel,
sample_id_map=sample_id_map))
elif opts.method == 'partial_mantel':
output_f = open(
path.join(opts.output_dir, 'partial_mantel_results.txt'), 'w')
output_f.write(
run_mantel_test('partial_mantel',
input_dm_fps,
distmats,
opts.num_permutations,
opts.tail_type,
comment_mantel_pmantel,
control_dm_fp=opts.control_dm,
control_dm=parse_distmat(open(
opts.control_dm, 'U')),
sample_id_map=sample_id_map))
elif opts.method == 'mantel_corr':
output_f = open(
path.join(opts.output_dir, 'mantel_correlogram_results.txt'), 'w')
result_str, correlogram_fps, correlograms = run_mantel_correlogram(
input_dm_fps,
distmats,
opts.num_permutations,
comment_corr,
opts.alpha,
sample_id_map=sample_id_map,
variable_size_distance_classes=opts.variable_size_distance_classes)
output_f.write(result_str)
for corr_fp, corr in zip(correlogram_fps, correlograms):
corr.savefig(path.join(opts.output_dir, corr_fp + opts.image_type),
format=opts.image_type)
output_f.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create the output dir if it doesn't already exist.
try:
if not path.exists(opts.output_dir):
create_dir(opts.output_dir)
except:
option_parser.error("Could not create or access output directory " "specified with the -o option.")
sample_id_map = None
if opts.sample_id_map_fp:
sample_id_map = dict([(k, v[0]) for k, v in fields_to_dict(open(opts.sample_id_map_fp, "U")).items()])
input_dm_fps = opts.input_dms
distmats = [parse_distmat(open(dm_fp, "U")) for dm_fp in input_dm_fps]
if opts.method == "mantel":
output_f = open(path.join(opts.output_dir, "mantel_results.txt"), "w")
output_f.write(
run_mantel_test(
"mantel",
input_dm_fps,
distmats,
opts.num_permutations,
opts.tail_type,
comment_mantel_pmantel,
sample_id_map=sample_id_map,
)
)
elif opts.method == "partial_mantel":
output_f = open(path.join(opts.output_dir, "partial_mantel_results.txt"), "w")
output_f.write(
run_mantel_test(
"partial_mantel",
input_dm_fps,
distmats,
opts.num_permutations,
opts.tail_type,
comment_mantel_pmantel,
control_dm_fp=opts.control_dm,
control_dm=parse_distmat(open(opts.control_dm, "U")),
sample_id_map=sample_id_map,
)
)
elif opts.method == "mantel_corr":
output_f = open(path.join(opts.output_dir, "mantel_correlogram_results.txt"), "w")
result_str, correlogram_fps, correlograms = run_mantel_correlogram(
input_dm_fps, distmats, opts.num_permutations, comment_corr, opts.alpha, sample_id_map=sample_id_map
)
output_f.write(result_str)
for corr_fp, corr in zip(correlogram_fps, correlograms):
corr.savefig(path.join(opts.output_dir, corr_fp + opts.image_type), format=opts.image_type)
output_f.close()
def test_run_mantel_test_single_matrix(self):
"""Test running mantel test on a single dm."""
exp = '# A sample comment.\nDM\tDM\tNumber of entries\tMantel r ' + \
'statistic\tp-value\tNumber of permutations\tTail type\n'
obs = run_mantel_test('mantel', [self.fp1], [self.dm3], self.num_perms,
'less', self.comment, 0.5)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test(self):
"""Test running mantel test on two distmats."""
exp = '# A sample comment.\nDM\tDM\tNumber of entries\tMantel r ' + \
'statistic\tp-value\tNumber of permutations\tTail type\n' + \
'foo.txt\tbar.txt\t\t.\t.\t\tgreater\n'
obs = run_mantel_test('mantel', [self.fp1, self.fp2],
[self.dm1, self.dm2], self.num_perms, self.tail_type,
self.comment, self.alpha)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_partial_mantel_sample_id_map(self):
"""Test running partial mantel test with incompatible dms to map."""
exp = '# A sample comment.\nDM\tDM\tCDM\tNumber of entries\tMantel' + \
' r statistic\tp-value\tNumber of permutations\tTail type\n' + \
'foo.txt\tbar.txt\tbaz.txt\t\t.\t.\t\tgreater\n'
obs = run_mantel_test('partial_mantel', [self.fp1, self.fp2],
[self.dm1, self.dm2], self.num_perms, self.tail_type,
self.comment, self.fp3, self.dm4, self.sample_id_map)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_partial_mantel_too_small(self):
"""Test running partial mantel test with incompatible dms."""
exp = '# A sample comment.\nDM\tDM\tCDM\tNumber of entries\t' + \
'Mantel r statistic\tp-value\tNumber of permutations\t' + \
'Tail type\nfoo.txt\tbar.txt\tbaz.txt\t\tToo few samples\n'
obs = run_mantel_test('partial_mantel', [self.fp1, self.fp2],
[self.dm1, self.dm2], self.num_perms, self.tail_type,
self.comment, self.fp3, self.dm4)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_partial_mantel(self):
"""Test running partial mantel test with two dms and a control dm."""
exp = '# A sample comment.\nDM\tDM\tCDM\tNumber of entries\t' + \
'Mantel r statistic\tp-value\tNumber of permutations\tTail ' + \
'type\nfoo.txt\tbar.txt\tbaz.txt\t\t.\t.\t\tgreater\n'
obs = run_mantel_test('partial_mantel', [self.fp1, self.fp2],
[self.dm1, self.dm2], self.num_perms, self.tail_type,
self.comment, self.fp3, self.dm3)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_too_small(self):
"""Test running mantel test on two distmats that are incompatible."""
exp = '# A sample comment.\nDM\tDM\tNumber of entries\tMantel r ' + \
'statistic\tp-value\tNumber of permutations\tTail type\nfoo.txt\t' + \
'bar.txt\t\tToo few samples\n'
obs = run_mantel_test('mantel', [self.fp1, self.fp2],
[self.dm3, self.dm4], self.num_perms, 'less',
self.comment, 0.5)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_sample_id_map(self):
"""Test running mantel test on two distmats that need IDs mapped."""
exp = '# A sample comment.\nDM\tDM\tNumber of entries\tMantel r ' + \
'statistic\tp-value\tNumber of permutations\tTail type\n' + \
'foo.txt\tbar.txt\t\t.\t.\t\tless\n'
obs = run_mantel_test('mantel', [self.fp1, self.fp2],
[self.dm3, self.dm4], self.num_perms, 'less',
self.comment, 0.5, sample_id_map=self.sample_id_map)
self.assertEqual(self.remove_nums(obs), exp)
def test_run_mantel_test_multiple(self):
"""Test running mantel test on three distmats."""
exp = (
"# A sample comment.\nDM\tDM\tNumber of entries\tMantel r "
+ "statistic\tp-value\tNumber of permutations\tTail type\n"
+ "foo.txt\tbar.txt\t\t.\t.\t\tgreater\nfoo.txt\tbaz.txt\t\t-."
+ "\t.\t\tgreater\nbar.txt\tbaz.txt\t\t-.\t.\t\tgreater\n"
)
obs = run_mantel_test(
"mantel",
[self.fp1, self.fp2, self.fp3],
[self.dm1, self.dm2, self.dm3],
self.num_perms,
self.tail_type,
self.comment,
self.alpha,
)
self.assertEqual(self.remove_nums(obs), exp)
