def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
mapping_field = opts.mapping_field
output_dir = opts.output_dir
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
create_dir(output_dir)
# split mapping file
mapping_f = open(mapping_fp, 'U')
for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field):
mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str)
open(mapping_output_fp, 'w').write(sub_mapping_s)
# split otu table
otu_table_base_name = splitext(split(otu_table_fp)[1])[0]
mapping_f = open(mapping_fp, 'U')
otu_table = load_table(otu_table_fp)
try:
for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata(
otu_table,
mapping_f,
mapping_field):
otu_table_output_fp = join(output_dir, '%s_%s.biom' % (
otu_table_base_name, fp_str))
write_biom_table(sub_otu_table_s, otu_table_output_fp)
except OTUTableSplitError as e:
option_parser.error(e)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
mapping_field = opts.mapping_field
output_dir = opts.output_dir
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
create_dir(output_dir)
# split mapping file
mapping_f = open(mapping_fp, 'U')
for fp_str, sub_mapping_s in split_mapping_file_on_field(mapping_f, mapping_field):
mapping_output_fp = join(output_dir, 'mapping_%s.txt' % fp_str)
open(mapping_output_fp, 'w').write(sub_mapping_s)
# split otu table
otu_table_base_name = splitext(split(otu_table_fp)[1])[0]
mapping_f = open(mapping_fp, 'U')
otu_table_f = open(otu_table_fp, 'U')
for fp_str, sub_otu_table_s in split_otu_table_on_sample_metadata(
otu_table_f,
mapping_f,
mapping_field):
otu_table_output_fp = join(
output_dir, '%s_%s.biom' %
(otu_table_base_name, fp_str))
open(otu_table_output_fp, 'w').write(sub_otu_table_s)
def test_split_otu_table_on_sample_metadata_exceptions(self):
# mapping file 3 has no sample identifiers matching the OTU table
with self.assertRaises(OTUTableSplitError):
a = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f3,
"Treatment"))
def test_split_otu_table_on_sample_metadata_extra_mapping_entries(self):
""" split_otu_table_on_sample_metadata functions as expected with extra mapping data """
actual = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f2,
"Treatment"))
actual = [(id_, e) for id_, e in actual]
exp = [(id_, parse_biom_table(e)) for id_, e in otu_table_exp1]
actual.sort()
exp.sort()
for a, e in zip(actual, exp):
self.assertTrue(a == e)
def test_split_otu_table_on_sample_metadata_extra_mapping_entries(self):
""" split_otu_table_on_sample_metadata functions as expected with extra mapping data """
actual = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f2,
"Treatment"))
actual = [(id_, parse_biom_table(e)) for id_, e in actual]
exp = [(id_, parse_biom_table(e)) for id_, e in otu_table_exp1]
actual.sort()
exp.sort()
for a, e in zip(actual, exp):
self.assertEqual(a, e, "OTU tables are not equal:\n%s\n%s" %
(format_biom_table(a[1]), format_biom_table(e[1])))
def test_split_otu_table_on_sample_metadata_extra_mapping_entries(self):
""" split_otu_table_on_sample_metadata functions as expected with extra mapping data """
actual = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f2,
"Treatment"))
actual = [(id_,parse_biom_table(e)) for id_, e in actual]
exp = [(id_,parse_biom_table(e)) for id_, e in otu_table_exp1]
actual.sort()
exp.sort()
for a,e in zip(actual,exp):
self.assertEqual(a,e,"OTU tables are not equal:\n%s\n%s" % \
(format_biom_table(a[1]),format_biom_table(e[1])))
def test_split_otu_table_on_sample_metadata(self):
""" split_otu_table_on_sample_metadata functions as expected with valid input """
actual = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f1,
"Treatment"))
for id_, e in actual:
try:
parse_biom_table(e)
except:
print e
actual = [(id_,parse_biom_table(e)) for id_, e in actual]
exp = [(id_,parse_biom_table(e)) for id_, e in otu_table_exp1]
actual.sort()
exp.sort()
for a,e in zip(actual,exp):
self.assertEqual(a,e,"OTU tables are not equal:\n%s\n%s" % \
(format_biom_table(a[1]),format_biom_table(e[1])))
def test_split_otu_table_on_sample_metadata(self):
""" split_otu_table_on_sample_metadata functions as expected with valid input """
actual = list(split_otu_table_on_sample_metadata(self.otu_table_f1,
self.mapping_f1,
"Treatment"))
for id_, e in actual:
try:
parse_biom_table(e)
except:
print e
actual = [(id_, parse_biom_table(e)) for id_, e in actual]
exp = [(id_, parse_biom_table(e)) for id_, e in otu_table_exp1]
actual.sort()
exp.sort()
for a, e in zip(actual, exp):
self.assertEqual(a, e, "OTU tables are not equal:\n%s\n%s" %
(format_biom_table(a[1]), format_biom_table(e[1])))
