def test_compute_index(self):
increased = set(['bar'])
decreased = set(['not bar'])
exp = [('S1', log(1 / 3)), ('S2', nan), ('S3', log(2 / 2))]
obs = sorted(compute_index(self.t1, increased, decreased, 'taxonomy'))
self.assertEqual(obs, exp)
decreased = set(['foo'])
increased = set(['bar'])
exp = [('S1', -inf), ('S2', log(2.0 / 2.0)), ('S3', log(2.0 / 4.0))]
obs = sorted(compute_index(self.t2, increased, decreased, 'taxonomy'))
self.assertEqual(obs, exp)
def test_compute_index(self):
increased = set(['bar'])
decreased = set(['not bar'])
exp = [('S1', log(1 / 3)), ('S2', nan), ('S3', log(2 / 2))]
obs = sorted(compute_index(self.t1, increased, decreased, 'taxonomy'))
self.assertEqual(obs, exp)
decreased = set(['foo'])
increased = set(['bar'])
exp = [('S1', -inf), ('S2', log(2.0 / 2.0)), ('S3', log(2.0 / 4.0))]
obs = sorted(compute_index(self.t2, increased, decreased, 'taxonomy'))
self.assertEqual(obs, exp)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.show_indices:
for idx_key in sorted(known_indices):
idx = known_indices[idx_key]
print "%s: %s, %s" % (idx_key, idx['name'], idx['source'])
print '\t', 'increased:'
print '\n'.join(['\t\t%s' % t for t in idx['increased']])
print '\t', 'decreased:'
print '\n'.join(['\t\t%s' % t for t in idx['decreased']])
exit(0)
if opts.index is not None and known_indices.get(opts.index) is None:
option_parser.error("%s is not a known index. Known indices are: %s" %
(opts.index, ','.join(known_indices.keys())))
if opts.index is not None and (opts.increased or opts.decreased):
option_parser.error("Cannot specify both an existing and custom index")
if opts.index is None and opts.increased is None and \
opts.decreased is None:
option_parser.error("Must specify an existing or custom index")
if opts.increased and opts.decreased is None:
option_parser.error("Must specify decreased taxa")
if opts.decreased and opts.increased is None:
option_parser.error("Must specify increased taxa")
if opts.index is not None:
name = opts.name if opts.name is not None else opts.index
increased = known_indices[opts.index]['increased']
decreased = known_indices[opts.index]['decreased']
else:
name = opts.name if opts.name is not None else 'index'
increased = set(opts.increased.split(','))
decreased = set(opts.decreased.split(','))
if opts.input is None:
option_parser.error("Input not specified")
if opts.output is None:
option_parser.error("Output not specified")
table = load_table(opts.input)
if opts.mapping_file:
mapping_file = open(opts.mapping_file, 'U')
output_file = TemporaryFile()
else:
mapping_file = None
output_file = open(opts.output, 'w')
output_file.write("#SampleID\t%s\n" % name)
for id_, value in compute_index(table, increased, decreased, opts.key):
output_file.write("%s\t%f\n" % (id_, value))
if opts.mapping_file:
output_file.seek(0)
mapping_data = MetadataMap.mergeMappingFiles(
[output_file, mapping_file], no_data_value=nan)
with open(opts.output, 'w') as f:
f.write(str(mapping_data))
output_file.close()
def test_compute_index_raises(self):
with self.assertRaises(KeyError):
next(compute_index(self.t1, set(['foo']), set(['bar']), 'missing'))
with self.assertRaises(ValueError):
next(compute_index(self.t1, set(['foo']), set(['x']), 'taxonomy'))
def test_compute_index_raises(self):
with self.assertRaises(KeyError):
next(compute_index(self.t1, set(['foo']), set(['bar']), 'missing'))
with self.assertRaises(ValueError):
next(compute_index(self.t1, set(['foo']), set(['x']), 'taxonomy'))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.show_indices:
for idx_key in sorted(known_indices):
idx = known_indices[idx_key]
print "%s: %s, %s" % (idx_key, idx['name'], idx['source'])
print '\t', 'increased:'
print '\n'.join(['\t\t%s' % t for t in idx['increased']])
print '\t', 'decreased:'
print '\n'.join(['\t\t%s' % t for t in idx['decreased']])
exit(0)
if opts.index is not None and known_indices.get(opts.index) is None:
option_parser.error("%s is not a known index. Known indices are: %s"
% (opts.index, ','.join(known_indices.keys())))
if opts.index is not None and (opts.increased or opts.decreased):
option_parser.error("Cannot specify both an existing and custom index")
if opts.index is None and opts.increased is None and \
opts.decreased is None:
option_parser.error("Must specify an existing or custom index")
if opts.increased and opts.decreased is None:
option_parser.error("Must specify decreased taxa")
if opts.decreased and opts.increased is None:
option_parser.error("Must specify increased taxa")
if opts.index is not None:
name = opts.name if opts.name is not None else opts.index
increased = known_indices[opts.index]['increased']
decreased = known_indices[opts.index]['decreased']
else:
name = opts.name if opts.name is not None else 'index'
increased = set(opts.increased.split(','))
decreased = set(opts.decreased.split(','))
if opts.input is None:
option_parser.error("Input not specified")
if opts.output is None:
option_parser.error("Output not specified")
table = load_table(opts.input)
if opts.mapping_file:
mapping_file = open(opts.mapping_file, 'U')
output_file = TemporaryFile()
else:
mapping_file = None
output_file = open(opts.output, 'w')
output_file.write("#SampleID\t%s\n" % name)
for id_, value in compute_index(table, increased, decreased, opts.key):
output_file.write("%s\t%f\n" % (id_, value))
if opts.mapping_file:
output_file.seek(0)
mapping_data = MetadataMap.mergeMappingFiles([output_file, mapping_file],
no_data_value=nan)
with open(opts.output, 'w') as f:
f.write(str(mapping_data))
output_file.close()