def test_alternate_range(self):
     assert parse_deltree('1:10') == \
         [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     assert parse_deltree('1,3,4:6') == \
         [1, 3, 4, 5, 6]
     assert parse_deltree('1,3,4:6,8,9:10') == \
         [1, 3, 4, 5, 6, 8, 9, 10]
Beispiel #2
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 def test_alternate_range(self):
     assert parse_deltree('1:10') == \
         [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     assert parse_deltree('1,3,4:6') == \
         [1, 3, 4, 5, 6]
     assert parse_deltree('1,3,4:6,8,9:10') == \
         [1, 3, 4, 5, 6, 8, 9, 10]
 def test_error(self):
     with self.assertRaises(ValueError):
         parse_deltree("1-x")
     with self.assertRaises(ValueError):
         parse_deltree("sausage")
     with self.assertRaises(ValueError):
         parse_deltree("first:last")
Beispiel #4
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 def test_error(self):
     with self.assertRaises(ValueError):
         parse_deltree("1-x")
     with self.assertRaises(ValueError):
         parse_deltree("sausage")
     with self.assertRaises(ValueError):
         parse_deltree("first:last")
 def test_simple(self):
     assert parse_deltree('1') == [1]
     assert parse_deltree('1,2,3') == [1, 2, 3]
     assert parse_deltree('1,3,5') == [1, 3, 5]
     assert parse_deltree('1-10') == \
         [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     assert parse_deltree('1,3,4-6') == \
         [1, 3, 4, 5, 6]
     assert parse_deltree('1,3,4-6,8,9-10') == \
         [1, 3, 4, 5, 6, 8, 9, 10]
Beispiel #6
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 def test_simple(self):
     assert parse_deltree('1') == [1]
     assert parse_deltree('1,2,3') == [1, 2, 3]
     assert parse_deltree('1,3,5') == [1, 3, 5]
     assert parse_deltree('1-10') == \
         [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     assert parse_deltree('1,3,4-6') == \
         [1, 3, 4, 5, 6]
     assert parse_deltree('1,3,4-6,8,9-10') == \
         [1, 3, 4, 5, 6, 8, 9, 10]
    newnexus = None

    if options.number:
        print_site_values(nexus)
        exit()
    
    if options.stats:
        print_character_stats(nexus)
        exit()
        
    const, unique, zeros, remove = [], [], [], []
    if options.constant:
        const = find_constant_sites(nexus)
        print("Constant Sites: %s" % ",".join([str(i) for i in const]))
    if options.unique:
        unique = find_unique_sites(nexus)
        print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
    if options.zeros:
        zeros = check_zeros(nexus)
        print("Zero Sites: %s" % ",".join([str(i) for i in zeros]))
    if options.remove:
        remove = [int(i) for i in parse_deltree(options.remove)]
        print("Remove: %s" % ",".join([str(i) for i in zeros]))
        
    newnexus = new_nexus_without_sites(nexus, set(const + unique + zeros + remove))
    
    # check for saving
    if newnexus is not None and newnexusname is not None:
        newnexus.write_to_file(newnexusname)
        print("New nexus written to %s" % newnexusname)