allpy: b556c96c6719 test/test

allpy

view test/test_markups.py @ 1168:b556c96c6719

blocks3d/www Makefile: never check certificates of github, they are too confusing for wget

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 26 May 2014 17:20:29 +0400
parents	0aa68678861c
children

line source

1 from StringIO import StringIO

2 from allpy import base

3 from allpy import protein

4 from allpy import markups

5 import protein_pdb

7 def test_index():

8 seq = protein.Sequence.from_string('SEQVENCE', name='sequence')

9 markup = seq.add_markup('index')

10 assert seq[5].index == 5

11 assert markup[seq[5]] == 5

13 def test_hardio():

14 aln = protein.Alignment().append_row_from_string("SEQVENCE", name="A")

15 markup = aln.sequences[0].add_markup('index')

16 del aln.columns[2]

18 file = StringIO()

19 aln.to_file(file, format="markup")

21 file.seek(0)

22 aln = protein.Alignment().append_file(file, format="markup")

23 assert str(aln.sequences[0]) == "SEVENCE"

24 assert aln.sequences[0][3].index == 3

26 def test_number():

27 seq = protein.Sequence.from_string('SEQVENCE', name='sequence')

28 seq.add_markup('number')

29 assert seq[5].number == 6

30 assert seq.markups["number"][seq[5]] == 6

32 try:

33 seq.add_markup('number')

34 except AssertionError:

35 pass

36 else:

37 raise AssertionError("Silently created same named alignment")

39 seq.add_markup('number', use_existing=True)

41 try:

42 other = markups.SequenceIndexMarkup

43 seq.add_markup('number', use_existing=True, markup_class=other)

44 except AssertionError:

45 pass

46 else:

47 raise AssertionError("Created same named different class alignment")

49 def test_case():

50 seq = protein.Sequence.from_string('seQVEncE', name='sequence')

51 seq.add_markup('case')

52 letters = ''.join(v[0] for v in seq.markups['case'].sorted_values())

53 assert letters == 'lluuullu'

55 fakefile = StringIO()

56 aln = protein.Alignment().append_sequence(seq)

57 aln.to_file(fakefile, format='markup')

59 fakefile.seek(0)

60 aln = protein.Alignment().append_file(fakefile, format='markup')

61 seq = aln.sequences[0]

62 letters = ''.join(v[0] for v in seq.markups['case'].sorted_values())

63 assert letters == 'lluuullu'

65 def test_manual():

66 seq = protein.Sequence.from_string('SEQVENCE', name='sequence')

67 markup = seq.add_markup(name='my_markup', markup_class=base.SequenceMarkup)

68 markup[seq[4]] = 5

69 assert seq[4].my_markup == 5

70 seq[2].my_markup = 4

71 assert markup[seq[2]] == 4

73 def test_by_name():

74 from_name = markups.by_name['sequence_markup', 'index']

75 assert from_name is markups.SequenceIndexMarkup

76 from_name = markups.by_name['alignment_markup', 'index']

77 assert from_name is markups.AlignmentIndexMarkup

79 def test_io():

80 aln = (protein.Alignment().

81 append_row_from_string('aseq-vence', name='a').

82 append_row_from_string('ase-qret--', name='b')

83 )

85 class MySequenceMarkup(base.SequenceMarkup, markups.IntMarkupMixin):

86 name = 'm1'

87 class MyAlignmentMarkup(base.AlignmentMarkup, markups.IntMarkupMixin):

88 name = 'm2'

89 markups.update(MySequenceMarkup, MyAlignmentMarkup)

91 s = aln.sequences[0]

92 c = aln.columns

93 m1 = s.add_markup('m1')

94 m1[s[5]] = 5

95 m1[s[3]] = 3

96 m2 = aln.add_markup('m2')

97 m2[c[5]] = 5

98 m2[c[6]] = 6

99 m3 = aln.add_markup('m3', markup_class=MyAlignmentMarkup)

100 m3.save = False

101 m3[c[1]] = "hello"

102 m4 = aln.add_markup('m4', markup_class=MyAlignmentMarkup)

103 m5 = s.add_markup('ss', markup_class=markups.SequenceCharMarkup)

104 s[0].ss = 'H'

105 s[5].ss = 'S'

106

107 file = StringIO()

108 aln.to_file(file, format='markup')

109

110 file.seek(0)

111 out = protein.Alignment().append_file(file, format='markup')

112 s = out.sequences[0]

113 c = out.columns

114 assert s[5].m1 == 5 and s[3].m1 == 3

115 assert out.<