allpy: 6134ae1dfdae allpy/markup.py

allpy

view allpy/markup.py @ 896:6134ae1dfdae

fix error caused by applying secondary structure markup This bug should be digged. For some reason BioPython's DSSP failed to get secondary structure information of a residue: $ ./pair_cores/pair_cores.py -i test/aln1.fasta -y aaa -e True ... ('A', (' ', 51, ' ')) caused by dssp.__getitem__

author	Boris Nagaev <bnagaev@gmail.com>
date	Fri, 23 Sep 2011 14:10:25 +0400
parents	3566d253c994
children

line source

1 import base

3 default = object()

4 """ object for use as key for default value """

6 class Markup(object):

7 """ Markup for Sequence or Alignment

9 container is iterable collection of items.

10 item is object getting markup data (new attribute).

12 container: Alignment, item: Column

13 container: Sequence, item: Monomer

15 Markup stored in attributes of item is internal value.

16 When export or import, it is mapped to or from external value.

17 Internal value could be of any type.

18 External value should be single character.

20 Data:

21 * name -- name (str) of attribute of object

22 * container

23 * map_out -- dict, mapping internal values to external

24 * map_in -- dict, mapping external values to internal

26 map_in and map_out can have key markup.default, which used when

27 input key is not in map. To drop this defaults, drop this key

28 from map_out and map_in dicts. In this case to_string() and

29 from_string() methods can raise KeyError

30 """

32 def __init__(self, name, container, map_out={}):

33 """ Note: add convenient defaults to maps """

34 self.name = name

35 self.container = container

36 self.set_map_out(map_out)

37 self.set_internal_default()

38 self.set_external_default()

40 def set_map_out(self, map_out):

41 self.map_out = map_out

42 self.map_in = dict([(v, k) for (k, v) in self.map_out.items()])

44 def set_map_in(self, map_in):

45 self.map_in = map_in

46 self.map_out = dict([(v, k) for (k, v) in self.map_in.items()])

48 def set_internal_default(self, default_value=None):

49 self.map_in[default] = default_value

51 def set_external_default(self, default_value='-'):

52 self.map_out[default] = default_value

54 def __getitem__(self, item):

55 """ return internal value for given item

57 markup[monomer] <==> monomer.name, where name is markup.name

58 """

59 return getattr(item, self.name)

61 def __setitem__(self, item, value):

62 """ set attribute of item to value """

63 setattr(item, self.name, value)

65 def __contains__(self, item):

66 """ return item has attribute

68 usage: if item in markup

69 """

70 return hasattr(item, self.name)

72 def clear(self):

73 """ delete all attributes from items """

74 for item in self.keys():

75 delattr(item, self.name)

77 def to_string(self):

78 """ return string representing markup """

79 internal_values = []

80 for item in self.container:

81 if item in self and self[item] in self.map_out:

82 internal_values.append(self[item])

83 else:

84 internal_values.append(default)

85 return ''.join(self.map_out[i] for i in internal_values)

87 @classmethod

88 def from_string(cls, string, name, container, map_out={}):

89 """ return new markup

91 add (or replaces) attributes to items

92 """

93 assert len(string) == len(container)

94 self = cls(name, container, map_out)

95 for char, item in zip(list(string), self.container):

96 if char in self.map_in:

97 internal = self.map_in[char]

98 else:

99 internal = self.map_in[default]

100 setattr(item, self.name, internal)

101 return self

102

103 def items(self):

104 """ return list of tuples (item, self[item]) for items with attribute """

105 for item in self.container:

106 if item in self:

107 yield (item, self[item])

108

109 def keys(self):

110 """ return list of items for with attribute is determined """

111 for item in self.container:

112 if item in self:

113 yield item

114