def test_make_non_empty_sample_lists(self):
"""Test that sample lists are created correctly."""
fields = ['color', 'temp']
obs_sgs, obs_vgs = make_non_empty_sample_lists(fields, self.mheaders,
self.mdata)
exp_sgs = [
array(['s4'], dtype='|S5'),
array(['s1'], dtype='|S5'),
array(['s0'], dtype='|S5'),
array(['s3'], dtype='|S5'),
array(['s2'], dtype='|S5')
]
exp_vgs = [('blue', '0'), ('blue', 'cold'), ('blue', 'hot'),
('cyan', 'hot'), ('green', 'cold')]
for i, j in zip(obs_sgs, exp_sgs):
assert_array_equal(i, j)
for i, j in zip(obs_vgs, exp_vgs):
assert_array_equal(i, j)
fields = ['color']
obs_sgs, obs_vgs = make_non_empty_sample_lists(fields, self.mheaders,
self.mdata)
exp_sgs = [
array(['s0', 's1', 's4'], dtype='|S5'),
array(['s3'], dtype='|S5'),
array(['s2'], dtype='|S5')
]
exp_vgs = [('blue', ), ('cyan', ), ('green', )]
for i, j in zip(obs_sgs, exp_sgs):
assert_array_equal(i, j)
for i, j in zip(obs_vgs, exp_vgs):
assert_array_equal(i, j)
def test_make_non_empty_sample_lists(self):
"""Test that sample lists are created correctly."""
fields = ['color', 'temp']
obs_sgs, obs_vgs = make_non_empty_sample_lists(fields, self.mheaders,
self.mdata)
exp_sgs = [array(['s4'], dtype='|S5'),
array(['s1'], dtype='|S5'),
array(['s0'], dtype='|S5'),
array(['s3'], dtype='|S5'),
array(['s2'], dtype='|S5')]
exp_vgs = [('blue', '0'),
('blue', 'cold'),
('blue', 'hot'),
('cyan', 'hot'),
('green', 'cold')]
for i,j in zip(obs_sgs, exp_sgs):
assert_array_equal(i, j)
for i,j in zip(obs_vgs, exp_vgs):
assert_array_equal(i, j)
fields = ['color']
obs_sgs, obs_vgs = make_non_empty_sample_lists(fields, self.mheaders,
self.mdata)
exp_sgs = [array(['s0', 's1', 's4'], dtype='|S5'),
array(['s3'], dtype='|S5'),
array(['s2'], dtype='|S5')]
exp_vgs = [('blue',), ('cyan',), ('green',)]
for i,j in zip(obs_sgs, exp_sgs):
assert_array_equal(i, j)
for i,j in zip(obs_vgs, exp_vgs):
assert_array_equal(i, j)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
biom_table_fp = opts.biom_table_fp
mapping_fp = opts.mapping_fp
fields = opts.fields.split(',')
output_dir = opts.output_dir
suppress_mf = opts.suppress_mapping_file_output
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
bt = load_table(biom_table_fp)
mdata, mheaders, mcomments = parse_mapping_file(mapping_fp)
mdata = array(mdata)
# check that biom file and mapping file have matching sample names. discard
# those samples that do not appear in both.
shared_samples = list(set(mdata[:, 0]).intersection(bt.ids(axis='sample')))
if len(shared_samples) == 0:
raise ValueError('Mapping file and biom table share no samples.')
elif len(shared_samples) == len(mdata[:, 0]):
mdata = array(mdata)
else:
# we want to preserve the order of the samples in the biom table
ss_bt_order = [s for s in bt.ids(axis='sample') if s in
shared_samples]
bt = bt.filter(ss_bt_order, axis='sample', inplace=True)
mdata = subset_mapping_data(mdata, shared_samples)
# check that headers in mapping data
if not all([i in mheaders for i in fields]):
raise ValueError('One or more of the specified fields was not found ' +\
'in the mapping file.')
# create output directory and create base names
create_dir(output_dir)
mf_base_name = join(output_dir, splitext(split(mapping_fp)[1])[0])
bt_base_name = join(output_dir, splitext(split(biom_table_fp)[1])[0])
# run code and append output
sample_groups, value_groups = make_non_empty_sample_lists(fields, mheaders,
mdata)
for sg, vg in zip(sample_groups, value_groups):
name_base = '__' + '%s_%s_' * len(vg) + '_'
name_tmp = []
for f, v in zip(fields, vg):
name_tmp.extend([f, v])
nb = name_base % tuple(name_tmp)
tmp_mf_data = subset_mapping_data(mdata, sg)
tmp_mf_str = format_mapping_file(mheaders, tmp_mf_data, mcomments)
write_biom_table(bt.filter(sg, axis='sample', inplace=False),
bt_base_name + nb + '.biom')
if not suppress_mf:
o = open(mf_base_name + nb + '.txt', 'w')
o.writelines(tmp_mf_str)
o.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
biom_table_fp = opts.biom_table_fp
mapping_fp = opts.mapping_fp
fields = opts.fields.split(',')
output_dir = opts.output_dir
suppress_mf = opts.suppress_mapping_file_output
# column_rename_ids = opts.column_rename_ids
# include_repeat_cols = opts.include_repeat_cols
bt = load_table(biom_table_fp)
mdata, mheaders, mcomments = parse_mapping_file(mapping_fp)
mdata = array(mdata)
# check that biom file and mapping file have matching sample names. discard
# those samples that do not appear in both.
shared_samples = list(set(mdata[:, 0]).intersection(bt.ids(axis='sample')))
if len(shared_samples) == 0:
raise ValueError('Mapping file and biom table share no samples.')
elif len(shared_samples) == len(mdata[:, 0]):
mdata = array(mdata)
else:
# we want to preserve the order of the samples in the biom table
ss_bt_order = [s for s in bt.ids(axis='sample') if s in
shared_samples]
bt = bt.filter(ss_bt_order, axis='sample', inplace=True)
mdata = subset_mapping_data(mdata, shared_samples)
# check that headers in mapping data
if not all([i in mheaders for i in fields]):
raise ValueError('One or more of the specified fields was not found ' +\
'in the mapping file.')
# create output directory and create base names
create_dir(output_dir)
mf_base_name = join(output_dir, splitext(split(mapping_fp)[1])[0])
bt_base_name = join(output_dir, splitext(split(biom_table_fp)[1])[0])
# run code and append output
sample_groups, value_groups = make_non_empty_sample_lists(fields, mheaders,
mdata)
for sg, vg in zip(sample_groups, value_groups):
name_base = '__' + '%s_%s_' * len(vg) + '_'
name_tmp = []
for f, v in zip(fields, vg):
name_tmp.extend([f, v])
nb = name_base % tuple(name_tmp)
tmp_mf_data = subset_mapping_data(mdata, sg)
tmp_mf_str = format_mapping_file(mheaders, tmp_mf_data, mcomments)
write_biom_table(bt.filter(sg, axis='sample', inplace=False),
bt_base_name + nb + '.biom')
if not suppress_mf:
o = open(mf_base_name + nb + '.txt', 'w')
o.writelines(tmp_mf_str)
o.close()
