allpy: a4d7438c142f test/test

allpy

view test/test_base.py @ 418:a4d7438c142f

add fileio module, remove fasta module, add msf support (see #31)

author	boris (netbook) <bnagaev@gmail.com>
date	Fri, 11 Feb 2011 15:04:17 +0300
parents	e70a40d7a993
children	364232e42888

line source

1 import allpy.base as b

2 import allpy.protein as p

3 from StringIO import StringIO

5 def test_new_monomers():

7 try:

8 m = b.Monomer.from_code1('A')

9 except Exception:

10 pass

11 else:

12 assert False, "base.Monomers must not be constructible from code1"

14 m = b.Monomer.from_code3('ALA')

15 assert m.__class__.__name__ == "Alanine"

16 assert m.code1 == "A"

17 assert m.code3 == "ALA"

18 assert m.name == "Alanine"

20 m = b.Monomer.from_name("alaNINE")

21 assert m.__class__.__name__ == "Alanine"

22 assert m.code1 == "A"

23 assert m.code3 == "ALA"

24 assert m.name == "Alanine"

26 def assert_alignment(alignment, *body):

27 s = StringIO()

28 alignment.to_file(s)

29 body = "".join([">\n%s\n" % string for string in body])

30 assert s.getvalue() == body, "Expected:\n%s\nGot:\n%s" % (body, s.getvalue())

32 def test_alignment_changes():

34 a = (p.Alignment().

35 append_row_from_string("a-------cdef").

36 append_row_from_string("ghiklmpq--").

37 append_row_from_string("-------------rst"))

39 assert_alignment(a,

40 "A-------CDEF----",

41 "GHIKLMPQ--------",

42 "-------------RST",

43 )

45 a.flush("left")

46 assert_alignment(a,

47 "ACDEF-----------",

48 "GHIKLMPQ--------",

49 "RST-------------",

50 )

52 a.flush("center")

53 assert_alignment(a,

54 "-----ACDEF------",

55 "----GHIKLMPQ----",

56 "------RST-------",

57 )

59 a.flush("right")

60 assert_alignment(a,

61 "-----------ACDEF",

62 "--------GHIKLMPQ",

63 "-------------RST",

64 )

66 a._wipe()

67 assert_alignment(a,

68 "----------------",

69 "----------------",

70 "----------------",

71 )

73 # vim: set et ts=4 sts=4 sw=4: