def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.input_path
otu_table = load_table(otu_table_fp)
sample_ids = otu_table.ids()
otu_ids = otu_table.ids(axis='observation')
# This is not memory safe: need to be able to load the otu table as ints
otu_table_array = array(list(otu_table.iter_data(axis='observation')),
dtype='int')
if opts.type_of_test == 'all_together':
type_of_test = TEST_ON_TREE
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_pair':
type_of_test = TEST_ON_PAIRWISE
header_text = "sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_sample':
type_of_test = TEST_ON_ENVS
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
if opts.significance_test == 'p-test':
raise RuntimeError(
'significance test type "each_sample" not allowed for p-test')
else:
raise RuntimeError('significance test type "%s" not found' %
opts.type_of_test)
# note, uses ugly temp file
if opts.significance_test == 'unweighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
try:
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted=False,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
except ValueError as e:
if e.message == ("No valid samples/environments found. Check"
" whether tree tips match otus/taxa present in"
" samples/environments"):
raise ValueError(e.message + " and that the otu abundance is"
" not relative.")
raise e
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#unweighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'p-test':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_p_test_file(tree_in,
envs_in,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#andy martin's p-test significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted=True,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#weighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_normalized_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted='correct',
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#weighted normalized unifrac significance test\n")
of.write(
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
else:
raise RuntimeError('significance test "%s" not found' %
opts.significance_test)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.tree_path==None:
if opts.significance_test in ['unweighted_unifrac','weighted_unifrac','p-test']:
raise RuntimeError('please supply a phylogenetic tree for %s' %\
opts.significance_test)
# note, uses ugly temp file
if opts.significance_test == 'unweighted_unifrac':
tree_in = open(opts.tree_path,'U')
otu_table_fp = opts.input_path
output_fp = opts.output_path + '_envs.tmp'
otu_table_lines = open(otu_table_fp, 'U')
sample_ids, otu_ids, otu_table_array, lineages = \
parse_otu_table(otu_table_lines)
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp,'U')
result = fast_unifrac_permutations_file(tree_in, envs_in,
weighted=False, num_iters=opts.num_iters, verbose=opts.verbose)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path,'w')
of.write(\
"#unweighted unifrac significance test\n")
of.write(\
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str,line)) + '\n')
of.close()
elif opts.significance_test == 'p-test':
tree_in = open(opts.tree_path,'U')
otu_table_fp = opts.input_path
output_fp = opts.output_path + '_envs.tmp'
otu_table_lines = open(otu_table_fp, 'U')
sample_ids, otu_ids, otu_table_array, lineages = \
parse_otu_table(otu_table_lines)
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp,'U')
result = fast_p_test_file(tree_in, envs_in,
num_iters=opts.num_iters, verbose=opts.verbose)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path,'w')
of.write(\
"#andy martin's p-test significance test\n")
of.write(\
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str,line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_unifrac':
tree_in = open(opts.tree_path,'U')
otu_table_fp = opts.input_path
output_fp = opts.output_path + '_envs.tmp'
otu_table_lines = open(otu_table_fp, 'U')
sample_ids, otu_ids, otu_table_array, lineages = \
parse_otu_table(otu_table_lines)
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp,'U')
result = fast_unifrac_permutations_file(tree_in, envs_in,
weighted=True, num_iters=opts.num_iters, verbose=opts.verbose)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path,'w')
of.write(\
"#weighted unifrac significance test\n")
of.write(\
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str,line)) + '\n')
of.close()
else:
raise RuntimeError('significance test "%s" not found' %\
opts.significance_test)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.input_path
otu_table = load_table(otu_table_fp)
sample_ids = otu_table.ids()
otu_ids = otu_table.ids(axis='observation')
# This is not memory safe: need to be able to load the otu table as ints
otu_table_array = array(list(otu_table.iter_data(axis='observation')),
dtype='int')
if opts.type_of_test == 'all_together':
type_of_test = TEST_ON_TREE
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_pair':
type_of_test = TEST_ON_PAIRWISE
header_text = "sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_sample':
type_of_test = TEST_ON_ENVS
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
if opts.significance_test == 'p-test':
raise RuntimeError(
'significance test type "each_sample" not allowed for p-test')
else:
raise RuntimeError('significance test type "%s" not found' %
opts.type_of_test)
# note, uses ugly temp file
if opts.significance_test == 'unweighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in, envs_in,
weighted=False, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#unweighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'p-test':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_p_test_file(tree_in, envs_in,
num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write(
"#andy martin's p-test significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in, envs_in,
weighted=True, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write(
"#weighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_normalized_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(
sample_ids, otu_ids, otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in, envs_in,
weighted='correct', num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write(
"#weighted normalized unifrac significance test\n")
of.write(
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
else:
raise RuntimeError('significance test "%s" not found' %
opts.significance_test)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_fp = opts.input_path
otu_table = parse_biom_table(open(otu_table_fp, 'U'))
sample_ids = otu_table.SampleIds
otu_ids = otu_table.ObservationIds
# This is not memory safe: need to be able to load the otu table as ints
otu_table_array = array(list(otu_table.iterObservationData()), dtype='int')
if opts.type_of_test == 'all_together':
type_of_test = TEST_ON_TREE
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_pair':
type_of_test = TEST_ON_PAIRWISE
header_text = "sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == 'each_sample':
type_of_test = TEST_ON_ENVS
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
if opts.significance_test == 'p-test':
raise RuntimeError(
'significance test type "each_sample" not allowed for p-test')
else:
raise RuntimeError('significance test type "%s" not found' %
opts.type_of_test)
# note, uses ugly temp file
if opts.significance_test == 'unweighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted=False,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#unweighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'p-test':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_p_test_file(tree_in,
envs_in,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#andy martin's p-test significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted=True,
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#weighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
elif opts.significance_test == 'weighted_normalized_unifrac':
tree_in = open(opts.tree_path, 'U')
output_fp = opts.output_path + '_envs.tmp'
result = format_unifrac_sample_mapping(sample_ids, otu_ids,
otu_table_array)
of = open(output_fp, 'w')
of.write('\n'.join(result))
of.close()
envs_in = open(output_fp, 'U')
result = fast_unifrac_permutations_file(tree_in,
envs_in,
weighted='correct',
num_iters=opts.num_iters,
verbose=opts.verbose,
test_on=type_of_test)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, 'w')
of.write("#weighted normalized unifrac significance test\n")
of.write(
"sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write('\t'.join(map(str, line)) + '\n')
of.close()
else:
raise RuntimeError('significance test "%s" not found' %
opts.significance_test)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.input_path
otu_table = parse_biom_table(open(otu_table_fp, "U"))
sample_ids = otu_table.SampleIds
otu_ids = otu_table.ObservationIds
## This is not memory safe: need to be able to load the otu table as ints
otu_table_array = array(list(otu_table.iterObservationData()), dtype="int")
if opts.type_of_test == "all_together":
type_of_test = TEST_ON_TREE
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == "each_pair":
type_of_test = TEST_ON_PAIRWISE
header_text = "sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n"
elif opts.type_of_test == "each_sample":
type_of_test = TEST_ON_ENVS
header_text = "sample\tp value\tp value (Bonferroni corrected)\n"
if opts.significance_test == "p-test":
raise RuntimeError('significance test type "each_sample" not allowed for p-test')
else:
raise RuntimeError('significance test type "%s" not found' % opts.type_of_test)
# note, uses ugly temp file
if opts.significance_test == "unweighted_unifrac":
tree_in = open(opts.tree_path, "U")
output_fp = opts.output_path + "_envs.tmp"
result = format_unifrac_sample_mapping(sample_ids, otu_ids, otu_table_array)
of = open(output_fp, "w")
of.write("\n".join(result))
of.close()
envs_in = open(output_fp, "U")
result = fast_unifrac_permutations_file(
tree_in, envs_in, weighted=False, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test
)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, "w")
of.write("#unweighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write("\t".join(map(str, line)) + "\n")
of.close()
elif opts.significance_test == "p-test":
tree_in = open(opts.tree_path, "U")
output_fp = opts.output_path + "_envs.tmp"
result = format_unifrac_sample_mapping(sample_ids, otu_ids, otu_table_array)
of = open(output_fp, "w")
of.write("\n".join(result))
of.close()
envs_in = open(output_fp, "U")
result = fast_p_test_file(
tree_in, envs_in, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test
)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, "w")
of.write("#andy martin's p-test significance test\n")
of.write(header_text)
for line in result:
of.write("\t".join(map(str, line)) + "\n")
of.close()
elif opts.significance_test == "weighted_unifrac":
tree_in = open(opts.tree_path, "U")
output_fp = opts.output_path + "_envs.tmp"
result = format_unifrac_sample_mapping(sample_ids, otu_ids, otu_table_array)
of = open(output_fp, "w")
of.write("\n".join(result))
of.close()
envs_in = open(output_fp, "U")
result = fast_unifrac_permutations_file(
tree_in, envs_in, weighted=True, num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test
)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, "w")
of.write("#weighted unifrac significance test\n")
of.write(header_text)
for line in result:
of.write("\t".join(map(str, line)) + "\n")
of.close()
elif opts.significance_test == "weighted_normalized_unifrac":
tree_in = open(opts.tree_path, "U")
output_fp = opts.output_path + "_envs.tmp"
result = format_unifrac_sample_mapping(sample_ids, otu_ids, otu_table_array)
of = open(output_fp, "w")
of.write("\n".join(result))
of.close()
envs_in = open(output_fp, "U")
result = fast_unifrac_permutations_file(
tree_in, envs_in, weighted="correct", num_iters=opts.num_iters, verbose=opts.verbose, test_on=type_of_test
)
envs_in.close()
os.remove(output_fp)
of = open(opts.output_path, "w")
of.write("#weighted normalized unifrac significance test\n")
of.write("sample 1\tsample 2\tp value\tp value (Bonferroni corrected)\n")
for line in result:
of.write("\t".join(map(str, line)) + "\n")
of.close()
else:
raise RuntimeError('significance test "%s" not found' % opts.significance_test)