def test_get_procrustes_results(self):
sample_id_map = {"CP3A1": "S1", "CC1A1": "S2", "CC2A1": "S3", "CP1A1": "S4"}
actual = get_procrustes_results(
StringIO(pcoa1_f), StringIO(pcoa1_f), sample_id_map=sample_id_map, randomize=None, max_dimensions=None
)
# just some sanity checks as the individual componenets are
# already tested -- these are based on looking at the output of the
# run, and testing to ensure that it hasn't changed
eigvals = array([8976580.24393, 6044862.67619, 4372581.39431, 3161360.10319, 2583594.45275, 2407555.39787])
prop_expl = array([23.1764657118, 15.6071186064, 11.2894866423, 8.16225689998, 6.67053450426, 6.21602253997])
site = array(
[
[-0.199225958574, -0.250846540029, -0.119813087305, -0.155652031006, 0.18495315824, -0.160875399364],
[-0.238263544222, -0.37724227779, -0.169458651217, 0.0305157004776, 0.112181007345, 0.0677415967093],
[0.116737988534, 0.414627960015, 0.201315243115, 0.113769076804, -0.283025353088, -0.144278863311],
[0.320751514262, 0.213460857804, 0.0879564954067, 0.0113672537238, -0.0141088124974, 0.237412665966],
]
)
site_ids = ["S3", "S2", "S1", "S4"]
expected = OrdinationResults(eigvals=eigvals, proportion_explained=prop_expl, site=site, site_ids=site_ids)
assert_almost_equal(actual[0].eigvals, expected.eigvals)
assert_almost_equal(actual[0].proportion_explained, expected.proportion_explained)
self.assertEqual(actual[0].site_ids, expected.site_ids)
assert_almost_equal(actual[0].site, expected.site)
assert_almost_equal(actual[1].eigvals, expected.eigvals)
assert_almost_equal(actual[1].proportion_explained, expected.proportion_explained)
assert_almost_equal(actual[1].site, expected.site)
self.assertEqual(actual[1].site_ids, expected.site_ids)
self.assertTrue(actual[2] < 6e-30)
def test_get_procrustes_results(self):
sample_id_map = {
'CP3A1': 'S1',
'CC1A1': 'S2',
'CC2A1': 'S3',
'CP1A1': 'S4'
}
actual = get_procrustes_results(StringIO(pcoa1_f),
StringIO(pcoa1_f),
sample_id_map=sample_id_map,
randomize=None,
max_dimensions=None)
# just some sanity checks as the individual componenets are
# already tested -- these are based on looking at the output of the
# run, and testing to ensure that it hasn't changed
eigvals = array([
8976580.24393, 6044862.67619, 4372581.39431, 3161360.10319,
2583594.45275, 2407555.39787
])
prop_expl = array([
23.1764657118, 15.6071186064, 11.2894866423, 8.16225689998,
6.67053450426, 6.21602253997
])
site = array([[
-0.199225958574, -0.250846540029, -0.119813087305, -0.155652031006,
0.18495315824, -0.160875399364
],
[
-0.238263544222, -0.37724227779, -0.169458651217,
0.0305157004776, 0.112181007345, 0.0677415967093
],
[
0.116737988534, 0.414627960015, 0.201315243115,
0.113769076804, -0.283025353088, -0.144278863311
],
[
0.320751514262, 0.213460857804, 0.0879564954067,
0.0113672537238, -0.0141088124974, 0.237412665966
]])
site_ids = ['S3', 'S2', 'S1', 'S4']
expected = OrdinationResults(eigvals=eigvals,
proportion_explained=prop_expl,
site=site,
site_ids=site_ids)
assert_almost_equal(actual[0].eigvals, expected.eigvals)
assert_almost_equal(actual[0].proportion_explained,
expected.proportion_explained)
self.assertEqual(actual[0].site_ids, expected.site_ids)
assert_almost_equal(actual[0].site, expected.site)
assert_almost_equal(actual[1].eigvals, expected.eigvals)
assert_almost_equal(actual[1].proportion_explained,
expected.proportion_explained)
assert_almost_equal(actual[1].site, expected.site)
self.assertEqual(actual[1].site_ids, expected.site_ids)
self.assertTrue(actual[2] < 6e-30)
def test_get_procrustes_results(self):
sample_id_map = {'CP3A1':'S1','CC1A1':'S2','CC2A1':'S3','CP1A1':'S4'}
actual = get_procrustes_results(self.pcoa1_f,self.pcoa1_f,\
sample_id_map=sample_id_map,randomize=None,max_dimensions=None)
# just some sanity checks as the individual componenets are
# already tested -- these are based on looking at the output of the
# run, and testing to ensure that it hasn't changed
self.assertEqual(set(actual[0].split('\n')),set('pc vector number\t1\t2\t3\t4\t5\t6\nS1\t0.116737988534\t0.414627960015\t0.201315243115\t0.113769076804\t-0.283025353088\t-0.144278863311\nS2\t-0.238263544222\t-0.37724227779\t-0.169458651217\t0.0305157004776\t0.112181007345\t0.0677415967093\nS3\t-0.199225958574\t-0.250846540029\t-0.119813087305\t-0.155652031006\t0.18495315824\t-0.160875399364\nS4\t0.320751514262\t0.213460857804\t0.0879564954067\t0.0113672537238\t-0.0141088124974\t0.237412665966\n\n\neigvals\t8976580.24393\t6044862.67619\t4372581.39431\t3161360.10319\t2583594.45275\t2407555.39787\n% variation explained\t23.1764657118\t15.6071186064\t11.2894866423\t8.16225689998\t6.67053450426\t6.21602253997'.split('\n')))
self.assertEqual(set(actual[1].split('\n')),set('pc vector number\t1\t2\t3\t4\t5\t6\nS1\t0.116737988534\t0.414627960015\t0.201315243115\t0.113769076804\t-0.283025353088\t-0.144278863311\nS2\t-0.238263544222\t-0.37724227779\t-0.169458651217\t0.0305157004776\t0.112181007345\t0.0677415967093\nS3\t-0.199225958574\t-0.250846540029\t-0.119813087305\t-0.155652031006\t0.18495315824\t-0.160875399364\nS4\t0.320751514262\t0.213460857804\t0.0879564954067\t0.0113672537238\t-0.0141088124974\t0.237412665966\n\n\neigvals\t8976580.24393\t6044862.67619\t4372581.39431\t3161360.10319\t2583594.45275\t2407555.39787\n% variation explained\t23.1764657118\t15.6071186064\t11.2894866423\t8.16225689998\t6.67053450426\t6.21602253997'.split('\n')))
self.assertTrue(actual[2] < 6e-30)
def test_get_procrustes_results(self):
sample_id_map = {'CP3A1':'S1','CC1A1':'S2','CC2A1':'S3','CP1A1':'S4'}
actual = get_procrustes_results(self.pcoa1_f,self.pcoa1_f,\
sample_id_map=sample_id_map,randomize=None,max_dimensions=None)
# just some sanity checks as the individual componenets are
# already tested -- these are based on looking at the output of the
# run, and testing to ensure that it hasn't changed
self.assertEqual(set(actual[0].split('\n')),set('pc vector number\t1\t2\t3\t4\t5\t6\nS1\t0.116737988534\t0.414627960015\t0.201315243115\t0.113769076804\t-0.283025353088\t-0.144278863311\nS2\t-0.238263544222\t-0.37724227779\t-0.169458651217\t0.0305157004776\t0.112181007345\t0.0677415967093\nS3\t-0.199225958574\t-0.250846540029\t-0.119813087305\t-0.155652031006\t0.18495315824\t-0.160875399364\nS4\t0.320751514262\t0.213460857804\t0.0879564954067\t0.0113672537238\t-0.0141088124974\t0.237412665966\n\n\neigvals\t8976580.24393\t6044862.67619\t4372581.39431\t3161360.10319\t2583594.45275\t2407555.39787\n% variation explained\t23.1764657118\t15.6071186064\t11.2894866423\t8.16225689998\t6.67053450426\t6.21602253997'.split('\n')))
self.assertEqual(set(actual[1].split('\n')),set('pc vector number\t1\t2\t3\t4\t5\t6\nS1\t0.116737988534\t0.414627960015\t0.201315243115\t0.113769076804\t-0.283025353088\t-0.144278863311\nS2\t-0.238263544222\t-0.37724227779\t-0.169458651217\t0.0305157004776\t0.112181007345\t0.0677415967093\nS3\t-0.199225958574\t-0.250846540029\t-0.119813087305\t-0.155652031006\t0.18495315824\t-0.160875399364\nS4\t0.320751514262\t0.213460857804\t0.0879564954067\t0.0113672537238\t-0.0141088124974\t0.237412665966\n\n\neigvals\t8976580.24393\t6044862.67619\t4372581.39431\t3161360.10319\t2583594.45275\t2407555.39787\n% variation explained\t23.1764657118\t15.6071186064\t11.2894866423\t8.16225689998\t6.67053450426\t6.21602253997'.split('\n')))
self.assertTrue(actual[2] < 6e-30)
def test_get_procrustes_results_imprefect_sample_overlap(self):
sample_id_map = {'aaa':'S0','bbb':'S1','ccc':'S2','ddd':'S3','eee':'S4'}
actual = get_procrustes_results(self.pcoa3_f,self.pcoa4_f,\
sample_id_map=sample_id_map,randomize=None,max_dimensions=None)
# Confirm that only the sample ids that are in both procrustes results
# show up in the output
for a in actual[:2]:
self.assertTrue('S1' in a)
self.assertTrue('S2' in a)
self.assertTrue('S3' in a)
self.assertTrue('S0' not in a)
self.assertTrue('S4' not in a)
def test_get_procrustes_results_imprefect_sample_overlap(self):
sample_id_map = {'aaa':'S0','bbb':'S1','ccc':'S2','ddd':'S3','eee':'S4'}
actual = get_procrustes_results(self.pcoa3_f,self.pcoa4_f,\
sample_id_map=sample_id_map,randomize=None,max_dimensions=None)
# Confirm that only the sample ids that are in both procrustes results
# show up in the output
for a in actual[:2]:
self.assertTrue('S1' in a)
self.assertTrue('S2' in a)
self.assertTrue('S3' in a)
self.assertTrue('S0' not in a)
self.assertTrue('S4' not in a)
def test_get_procrustes_results_imprefect_sample_overlap(self):
sample_id_map = {"aaa": "S0", "bbb": "S1", "ccc": "S2", "ddd": "S3", "eee": "S4"}
actual = get_procrustes_results(
StringIO(pcoa3_f), StringIO(pcoa4_f), sample_id_map=sample_id_map, randomize=None, max_dimensions=None
)
# Confirm that only the sample ids that are in both procrustes results
# show up in the output
for a in actual[:2]:
self.assertTrue("S1" in a.site_ids)
self.assertTrue("S2" in a.site_ids)
self.assertTrue("S3" in a.site_ids)
self.assertTrue("S0" not in a.site_ids)
self.assertTrue("S4" not in a.site_ids)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_fps = opts.input_fps
sample_id_map_fps = opts.sample_id_map_fps
num_dimensions = opts.num_dimensions
max_dims_str = str(num_dimensions or 'alldim')
output_dir = opts.output_dir
random_trials = opts.random_trials
if random_trials is not None and random_trials < 10:
option_parser.error(
'Must perform >= 10 trails for Monte Carlo analysis.')
if sample_id_map_fps and \
(len(sample_id_map_fps) + 1) != len(opts.input_fps):
option_parser.error('If providing sample id maps, there must be '
'exactly one fewer sample id maps than input '
'coordinate matrices.')
if not exists(output_dir):
makedirs(output_dir)
reference_input_fp = input_fps[0]
reference_input_fp_dir, input_fn1 = split(reference_input_fp)
reference_input_fp_basename, reference_input_fp_ext = splitext(input_fn1)
output_summary_fp = join(output_dir, 'procrustes_results.txt')
summary_file_lines = [
'#FP1\tFP2\tNum included dimensions\tMonte Carlo '
'p-value\tCount better\tM^2',
'#Warning: p-values in this file are NOT currently '
'adjusted for multiple comparisons.'
]
for i, query_input_fp in enumerate(input_fps[1:]):
query_input_fp_dir, query_input_fn = split(query_input_fp)
query_input_fp_basename, query_input_fp_ext = splitext(query_input_fn)
output_matrix1_fp = join(
output_dir,
'%s_transformed_reference.txt' % reference_input_fp_basename)
output_matrix2_fp = join(
output_dir,
'%s_transformed_q%d.txt' % (query_input_fp_basename, i + 1))
if sample_id_map_fps:
with open(sample_id_map_fps[i], "U") as f:
sample_id_map = dict([
(k, v[0]) for k, v in fields_to_dict(f).iteritems()
])
else:
sample_id_map = None
with open(reference_input_fp, 'U') as ref_in_f:
with open(query_input_fp, 'U') as query_in_f:
transf_coords1, transf_coords2, m_squared, rand_coords2 =\
get_procrustes_results(ref_in_f, query_in_f,
sample_id_map=sample_id_map,
randomize=False,
max_dimensions=num_dimensions)
transf_coords1.write(output_matrix1_fp)
transf_coords2.write(output_matrix2_fp)
if random_trials:
if opts.store_trial_details:
trial_output_dir = join(output_dir, 'trial_details_%d' % i + 2)
else:
trial_output_dir = None
coords_f1 = open(reference_input_fp, 'U')
coords_f2 = open(query_input_fp, 'U')
actual_m_squared, trial_m_squareds, count_better, mc_p_value =\
procrustes_monte_carlo(coords_f1,
coords_f2,
trials=random_trials,
max_dimensions=num_dimensions,
sample_id_map=sample_id_map,
trial_output_dir=trial_output_dir)
# truncate the p-value to the correct number of significant
# digits
mc_p_value_str = format_p_value_for_num_iters(
mc_p_value, random_trials)
summary_file_lines.append(
'%s\t%s\t%s\t%s\t%d\t%1.3f' %
(reference_input_fp, query_input_fp, max_dims_str,
mc_p_value_str, count_better, actual_m_squared))
else:
summary_file_lines.append(
'%s\t%s\t%s\tNA\tNA\t%1.3f' %
(reference_input_fp, query_input_fp, max_dims_str, m_squared))
# Write output summary
with open(output_summary_fp, 'w') as f:
f.write('\n'.join(summary_file_lines))
f.write('\n')
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_fps = opts.input_fps
sample_id_map_fps = opts.sample_id_map_fps
num_dimensions = opts.num_dimensions
max_dims_str = str(num_dimensions or 'alldim')
output_dir = opts.output_dir
random_trials = opts.random_trials
if random_trials != None and random_trials < 10:
option_parser.error('Must perform >= 10 trails for Monte Carlo analysis.')
if sample_id_map_fps and \
(len(sample_id_map_fps) + 1) != len(opts.input_fps):
option_parser.error('If providing sample id maps, there must be exactly'
' one fewer sample id maps than input coordinate'
' matrices.')
if not exists(output_dir):
makedirs(output_dir)
reference_input_fp = input_fps[0]
reference_input_fp_dir, input_fn1 = split(reference_input_fp)
reference_input_fp_basename, reference_input_fp_ext = splitext(input_fn1)
output_summary_fp = join(output_dir,'procrustes_results.txt')
summary_file_lines = \
['#FP1\tFP2\tNum included dimensions\tMonte Carlo p-value\tCount better\tM^2',
'#Warning: p-values in this file are NOT currently adjusted for multiple comparisons.']
for i,query_input_fp in enumerate(input_fps[1:]):
query_input_fp_dir, query_input_fn = split(query_input_fp)
query_input_fp_basename, query_input_fp_ext = splitext(query_input_fn)
output_matrix1_fp = join(output_dir,
'%s_transformed_reference.txt' % reference_input_fp_basename)
output_matrix2_fp = join(output_dir,\
'%s_transformed_q%d.txt' % (query_input_fp_basename, i+1))
if sample_id_map_fps:
sample_id_map = dict([(k,v[0]) \
for k,v in fields_to_dict(open(sample_id_map_fps[i], "U")).items()])
else:
sample_id_map = None
transformed_coords1, transformed_coords2, m_squared, randomized_coords2 =\
get_procrustes_results(open(reference_input_fp,'U'),\
open(query_input_fp,'U'),\
sample_id_map=sample_id_map,\
randomize=False,
max_dimensions=num_dimensions)
output_matrix1_f = open(output_matrix1_fp,'w')
output_matrix1_f.write(transformed_coords1)
output_matrix1_f.close()
output_matrix2_f = open(output_matrix2_fp,'w')
output_matrix2_f.write(transformed_coords2)
output_matrix2_f.close()
if random_trials:
if opts.store_trial_details:
trial_output_dir = join(output_dir,'trial_details_%d' % i+2)
else:
trial_output_dir = None
coords_f1 = list(open(reference_input_fp,'U'))
coords_f2 = list(open(query_input_fp,'U'))
actual_m_squared, trial_m_squareds, count_better, mc_p_value =\
procrustes_monte_carlo(coords_f1,
coords_f2,
trials=random_trials,
max_dimensions=num_dimensions,
sample_id_map=sample_id_map,
trial_output_dir=trial_output_dir)
# truncate the p-value to the correct number of significant
# digits
mc_p_value_str = format_p_value_for_num_iters(mc_p_value, random_trials)
summary_file_lines.append('%s\t%s\t%s\t%s\t%d\t%1.3f' %\
(reference_input_fp, query_input_fp, max_dims_str, mc_p_value_str,\
count_better, actual_m_squared))
else:
summary_file_lines.append('%s\t%s\t%s\tNA\tNA\t%1.3f' %\
(reference_input_fp, query_input_fp, max_dims_str, m_squared))
# Write output summary
f = open(output_summary_fp,'w')
f.write('\n'.join(summary_file_lines))
f.write('\n')
f.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
random_trials = opts.random_trials
if random_trials != None and random_trials < 10:
option_parser.error('Must perform >= 10 trails for Monte Carlo analysis.')
output_dir = opts.output_dir
sample_id_map_fp = opts.sample_id_map_fp
num_dimensions = opts.num_dimensions
if not exists(output_dir):
makedirs(output_dir)
if opts.store_trial_details:
trial_output_dir = '%s/trial_details/' % output_dir
else:
trial_output_dir = None
input_fp1 = opts.input_fps[0]
input_fp2 = opts.input_fps[1]
input_fp1_dir, input_fn1 = split(input_fp1)
input_fp1_basename, input_fp1_ext = splitext(input_fn1)
input_fp2_dir, input_fn2 = split(input_fp2)
input_fp2_basename, input_fp2_ext = splitext(input_fn2)
output_summary_fp = '%s/%s_%s_procrustes_results.txt' %\
(output_dir,input_fp1_basename,input_fp2_basename)
output_matrix1_fp = '%s/pc1_transformed.txt' % output_dir
output_matrix2_fp = '%s/pc2_transformed.txt' % output_dir
if sample_id_map_fp:
sample_id_map = dict([(k,v[0]) \
for k,v in fields_to_dict(open(sample_id_map_fp, "U")).items()])
else:
sample_id_map = None
transformed_coords1, transformed_coords2, m_squared, randomized_coords2 =\
get_procrustes_results(open(input_fp1,'U'),\
open(input_fp2,'U'),\
sample_id_map=sample_id_map,\
randomize=False,
max_dimensions=num_dimensions)
output_matrix1_f = open(output_matrix1_fp,'w')
output_matrix1_f.write(transformed_coords1)
output_matrix1_f.close()
output_matrix2_f = open(output_matrix2_fp,'w')
output_matrix2_f.write(transformed_coords2)
output_matrix2_f.close()
if random_trials:
summary_file_lines = ['FP1 FP2 Included_dimensions MC_p_value Count_better M^2']
coords_f1 = list(open(input_fp1,'U'))
coords_f2 = list(open(input_fp2,'U'))
actual_m_squared, trial_m_squareds, count_better, mc_p_value =\
procrustes_monte_carlo(coords_f1,\
coords_f2,\
trials=random_trials,\
max_dimensions=num_dimensions,
sample_id_map=sample_id_map,
trial_output_dir=trial_output_dir)
# truncate the p-value to the correct number of significant
# digits
mc_p_value_str = format_p_value_for_num_iters(mc_p_value, random_trials)
max_dims_str = str(num_dimensions or 'alldim')
summary_file_lines.append('%s %s %s %s %d %1.3f' %\
(input_fp1, input_fp2, str(max_dims_str), mc_p_value_str,\
count_better, actual_m_squared))
f = open(output_summary_fp,'w')
f.write('\n'.join(summary_file_lines))
f.write('\n')
f.close()