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1 #!/usr/bin/env python
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2
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3 from OrderedDict import OrderedDict
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4
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5 class Individual(object):
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6 __slots__ = ['_column', '_name', '_alias']
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7
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8 def __init__(self, column, name, alias=None):
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9 self._column = column
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10 self._name = name
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11 self._alias = alias
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12
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13 @property
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14 def column(self):
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15 return self._column
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16
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17 @property
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18 def name(self):
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19 return self._name if self._alias is None else self._alias
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20
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21 @property
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22 def alias(self):
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23 return self._alias
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24
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25 @alias.setter
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26 def alias(self, alias):
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27 self._alias = alias
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28
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29 @property
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30 def real_name(self):
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31 return self._name
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32
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33 def __eq__(self, other):
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34 return self._column == other._column and self._name == other._name
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35
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36 def __ne__(self, other):
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37 return not self.__eq__(other)
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38
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39 def __repr__(self):
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40 return 'Individual: column={0} name={1} alias={2}'.format(self._column, self._name, self._alias)
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41
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42
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43 class Population(object):
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44 def __init__(self, name=None):
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45 self._columns = OrderedDict()
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46 self._name = name
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47
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48 @property
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49 def name(self):
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50 return self._name
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51
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52 @name.setter
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53 def name(self, name):
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54 self._name = name
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55
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56 def add_individual(self, individual, alias=None):
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57 if individual.column not in self._columns:
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58 self._columns[individual.column] = individual
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59 elif self._columns[individual.column] == individual:
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60 # should should this be an error?
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61 # should we replace the alias using this entry?
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62 pass
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63 else:
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64 raise 'Duplicate column: {0}'.format(individual)
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65
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66 def is_superset(self, other):
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67 for column, other_individual in other._columns.items():
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68 our_individual = self._columns.get(column)
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69 if our_individual is None or our_individual != other_individual:
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70 return False
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71 return True
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72
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73 def is_disjoint(self, other):
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74 for column, our_individual in self._columns.items():
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75 other_individual = other._columns.get(column)
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76 if other_individual is not None and other_individual == our_individual:
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77 return False
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78 return True
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79
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80 def column_list(self):
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81 return self._columns.keys()
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82
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83 def individual_with_column(self, column):
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84 if column in self._columns:
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85 return self._columns[column]
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86 return None
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87
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88 def tag_list(self, delimiter=':'):
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89 entries = []
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90 for column, individual in self._columns.items():
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91 entry = '{0}{1}{2}'.format(column, delimiter, individual.name)
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92 entries.append(entry)
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93 return entries
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94
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95 def to_string(self, delimiter=':', separator=' ', replace_names_with=None):
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96 entries = []
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97 for column, individual in self._columns.items():
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98 value = individual.name
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99 if replace_names_with is not None:
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100 value = replace_names_with
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101 entry = '{0}{1}{2}'.format(column, delimiter, value)
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102 entries.append(entry)
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103 return separator.join(entries)
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104
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105 def __str__(self):
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106 return self.to_string()
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107
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108 def from_population_file(self, filename):
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109 with open(filename) as fh:
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110 for line in fh:
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111 line = line.rstrip('\r\n')
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112 column, name, alias = line.split('\t')
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113 alias = alias.strip()
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114 individual = Individual(column, name)
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115 if alias:
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116 individual.alias = alias
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117 self.add_individual(individual)
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118
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119 def from_tag_list(self, tag_list):
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120 for tag in tag_list:
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121 column, name = tag.split(':')
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122 individual = Individual(column, name)
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123 self.add_individual(individual)
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124
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125 def individual_names(self):
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126 for column, individual in self._columns.items():
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127 yield individual.name
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128
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