def test_run_mantel_correlogram_single_matrix(self):
"""Test running mantel correlogram on one dm."""
exp = ('# A sample comment.\nDM\tDM\tNumber of entries\tNumber of '
'permutations\tClass index\tNumber of distances\tMantel r statistic\t'
'p-value\tp-value (Bonferroni corrected)\tTail type\n', [], 0)
obs = run_mantel_correlogram([self.fp1], [self.dm1], self.num_perms,
self.comment, self.alpha, sample_id_map=self.sample_id_map)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
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 test_run_mantel_correlogram_too_small(self):
"""Test running mantel correlogram on two incompatible dms."""
exp = ('# A sample comment.\nDM\tDM\tNumber of entries\tNumber of '
'permutations\tClass index\tNumber of distances\tMantel r statistic\t'
'p-value\tp-value (Bonferroni corrected)\tTail type\nfoo.txt\tbaz.txt'
'\t\tToo few samples\n', [], 0)
obs = run_mantel_correlogram([self.fp1, self.fp3],
[self.dm2, self.dm4], self.num_perms, self.comment, self.alpha)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
def test_run_mantel_correlogram_no_comment(self):
"""Test running mantel correlogram without supplying a comment."""
exp = ('DM\tDM\tNumber of entries\tNumber of permutations\tClass index'
'\tNumber of distances\tMantel r statistic\tp-value\tp-value '
'(Bonferroni corrected)\tTail type\nfoo.txt\tbar.txt\t\t\t.\t\t-.\t.'
'\t.\tless\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n\t\t\t\t.\t\tNone\t'
'None\tNone\tNone\n', ['foo.txt_AND_bar.txt_mantel_correlogram.'], 1)
obs = run_mantel_correlogram([self.fp1, self.fp2],
[self.dm1, self.dm3], self.num_perms, None, self.alpha,
sample_id_map=self.sample_id_map)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
def test_run_mantel_correlogram(self):
"""Test running mantel correlogram on two distmats."""
exp = ('# A sample comment.\nDM\tDM\tNumber of entries\tNumber of '
'permutations\tClass index\tNumber of distances\tMantel r statistic\t'
'p-value\tp-value (Bonferroni corrected)\tTail type\nfoo.txt\tbar.txt'
'\t\t\t.\t\t.\t.\t.\tgreater\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n\t'
'\t\t\t.\t\tNone\tNone\tNone\tNone\n',
['foo.txt_AND_bar.txt_mantel_correlogram.'], 1)
obs = run_mantel_correlogram([self.fp1, self.fp2],
[self.dm1, self.dm2], self.num_perms, self.comment, self.alpha)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
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_correlogram_sample_id_map(self):
"""Test running mantel correlogram on two dms that need IDs mapped."""
exp = (
"# A sample comment.\nDM\tDM\tNumber of entries\tNumber of "
"permutations\tClass index\tNumber of distances\tMantel r "
"statistic\tp-value\tp-value (Bonferroni corrected)\tTail type"
"\nfoo.txt\tbar.txt\t\t\t.\t\t.\t.\t.\tgreater\n\t\t\t\t.\t\t"
"None\tNone\tNone\tNone\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n",
["foo.txt_AND_bar.txt_mantel_correlogram."],
1,
)
obs = run_mantel_correlogram(
[self.fp1, self.fp2],
[self.dm3, self.dm4],
self.num_perms,
self.comment,
self.alpha,
sample_id_map=self.sample_id_map,
)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
def test_run_mantel_correlogram_multiple(self):
"""Test running mantel correlogram on three distmats."""
exp = (
"# A sample comment.\nDM\tDM\tNumber of entries\tNumber of "
"permutations\tClass index\tNumber of distances\tMantel r statistic\t"
"p-value\tp-value (Bonferroni corrected)\tTail type\nfoo.txt\tbar.txt"
"\t\t\t.\t\t.\t.\t.\tgreater\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n\t"
"\t\t\t.\t\tNone\tNone\tNone\tNone\nfoo.txt\tbaz.txt\t\t\t.\t\t-.\t.\t"
".\tless\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n\t\t\t\t.\t\tNone\tNone"
"\tNone\tNone\nbar.txt\tbaz.txt\t\t\t.\t\t-.\t.\t.\tless\n\t\t\t\t.\t"
"\tNone\tNone\tNone\tNone\n\t\t\t\t.\t\tNone\tNone\tNone\tNone\n",
[
"foo.txt_AND_bar.txt_mantel_correlogram.",
"foo.txt_AND_baz.txt_mantel_correlogram.",
"bar.txt_AND_baz.txt_mantel_correlogram.",
],
3,
)
obs = run_mantel_correlogram(self.fps, self.distmats, self.num_perms, self.comment, self.alpha)
self.assertEqual((self.remove_nums(obs[0]), obs[1], len(obs[2])), exp)
