def test_verify_subset(self):
metadata = [('a','other stuff\tfoo'), ('b', 'asdasdasd'),
('c','123123123')]
table = table_factory(array([[1,2,3],[4,5,6]]), ['a','b','c'], ['x','y'])
self.assertTrue(verify_subset(table, metadata))
table = table_factory(array([[1,2],[3,4]]), ['a','b'], ['x','y'])
self.assertTrue(verify_subset(table, metadata))
table = table_factory(array([[1,2,3],[4,5,6]]), ['a','b','x'], ['x','y'])
self.assertFalse(verify_subset(table, metadata))
def test_verify_subset(self):
metadata = [('a','other stuff\tfoo'), ('b', 'asdasdasd'),
('c','123123123')]
table = table_factory(array([[1,2,3],[4,5,6]]), ['a','b','c'], ['x','y'])
self.assertTrue(verify_subset(table, metadata))
table = table_factory(array([[1,2],[3,4]]), ['a','b'], ['x','y'])
self.assertTrue(verify_subset(table, metadata))
table = table_factory(array([[1,2,3],[4,5,6]]), ['a','b','x'], ['x','y'])
self.assertFalse(verify_subset(table, metadata))
__copyright__ = "Copyright 2013, The American Gut Project"
__credits__ = ["Daniel McDonald"]
__license__ = "BSD"
__version__ = "unversioned"
__maintainer__ = "Daniel McDonald"
__email__ = "*****@*****.**"
if __name__ == '__main__':
if len(argv) != 4:
print "usage: python %s mappingfile table output" % argv[0]
exit(1)
header, mapping_file = parse_mapping_file(open(argv[1]))
table = load_table(argv[2])
if not verify_subset(table, mapping_file):
print "****"
print set([i[0] for i in mapping_file]) - set(table.ids())
print set(table.ids()) - set([i[0] for i in mapping_file])
raise ValueError("The table is not a subset of the mapping file!")
sliced = slice_mapping_file(table, mapping_file)
f = open(argv[3], 'w')
f.write(header)
f.write('\n')
f.write('\n'.join(sliced))
f.write('\n')
f.close()
__credits__ = ["Daniel McDonald"]
__license__ = "BSD"
__version__ = "unversioned"
__maintainer__ = "Daniel McDonald"
__email__ = "*****@*****.**"
if __name__ == "__main__":
if len(argv) != 4:
print "usage: python %s mappingfile table output" % argv[0]
exit(1)
header, mapping_file = parse_mapping_file(open(argv[1]))
table = load_table(argv[2])
if not verify_subset(table, mapping_file):
print "****"
print set([i[0] for i in mapping_file]) - set(table.ids())
print set(table.ids()) - set([i[0] for i in mapping_file])
raise ValueError("The table is not a subset of the mapping file!")
sliced = slice_mapping_file(table, mapping_file)
f = open(argv[3], "w")
f.write(header)
f.write("\n")
f.write("\n".join(sliced))
f.write("\n")
f.close()
