annotate Population.py @ 36:51cd0307fb70

Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents 8997f2ca8c7a
children
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1 #!/usr/bin/env python
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2
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3 import OrderedDict
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4 import base64
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5 import json
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6 import zlib
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8 import sys
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9
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10 class Individual(object):
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11 __slots__ = ['_column', '_name', '_alias']
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12
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13 def __init__(self, column, name, alias=None):
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14 self._column = int(column)
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15 self._name = name
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16 self._alias = alias
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17
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18 @property
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19 def column(self):
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20 return self._column
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21
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22 @property
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23 def name(self):
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24 return self._name if self._alias is None else self._alias
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25
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26 @property
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27 def alias(self):
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28 return self._alias
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29
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30 @alias.setter
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31 def alias(self, alias):
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32 self._alias = alias
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33
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34 @property
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35 def real_name(self):
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36 return self._name
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37
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38 def __eq__(self, other):
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39 return self._column == other._column and self._name == other._name
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40
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41 def __ne__(self, other):
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42 return not self.__eq__(other)
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43
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44 def __repr__(self):
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45 return 'Individual: column={0} name={1} alias={2}'.format(self._column, self._name, self._alias)
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46
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47
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48 class Population(object):
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49 def __init__(self, name=None):
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50 self._columns = OrderedDict.OrderedDict()
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51 self._name = name
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52
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53 @property
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54 def name(self):
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55 return self._name
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56
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57 @name.setter
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58 def name(self, name):
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59 self._name = name
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60
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61 def add_individual(self, individual, alias=None):
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62 if individual.column not in self._columns:
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63 self._columns[individual.column] = individual
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64 elif self._columns[individual.column] == individual:
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65 # should should this be an error?
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66 # should we replace the alias using this entry?
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67 pass
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68 else:
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69 raise 'Duplicate column: {0}'.format(individual)
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70
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71 def is_superset(self, other):
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72 for column, other_individual in other._columns.items():
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73 our_individual = self._columns.get(column)
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74 if our_individual is None or our_individual != other_individual:
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75 return False
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76 return True
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77
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78 def is_disjoint(self, other):
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79 for column, our_individual in self._columns.items():
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80 other_individual = other._columns.get(column)
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81 if other_individual is not None and other_individual == our_individual:
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82 return False
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83 return True
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84
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85 def column_list(self):
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86 return self._columns.keys()
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87
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88 def individual_with_column(self, column):
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89 if column in self._columns:
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90 return self._columns[column]
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91 return None
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92
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93 def tag_list(self, delimiter=':'):
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94 entries = []
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95 for column, individual in self._columns.iteritems():
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96 first_token = individual.name.split()[0]
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97 entry = '{0}{1}{2}'.format(column, delimiter, first_token)
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98 entries.append(entry)
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99 return entries
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100
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101 def to_string(self, delimiter=':', separator=' ', replace_names_with=None):
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102 entries = []
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103 for column, individual in self._columns.items():
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104 value = individual.name
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105 if replace_names_with is not None:
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106 value = replace_names_with
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107 entry = '{0}{1}{2}'.format(column, delimiter, value)
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108 entries.append(entry)
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109 return separator.join(entries)
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110
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111 def __str__(self):
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112 return self.to_string()
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113
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114 def from_population_file(self, filename):
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115 with open(filename) as fh:
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116 for line in fh:
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117 line = line.rstrip('\r\n')
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118 column, name, alias = line.split('\t')
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119 alias = alias.strip()
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120 individual = Individual(column, name)
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121 if alias:
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122 individual.alias = alias
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123 self.add_individual(individual)
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124
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125 def from_tag_list(self, tag_list):
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126 for tag in tag_list:
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127 column, name = tag.split(':')
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128 individual = Individual(column, name)
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129 self.add_individual(individual)
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130
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131 def from_wrapped_dict(self, wrapped_dict):
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132 unwraped_dict = self.unwrap_dict(wrapped_dict)
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133 for name, column in unwraped_dict.iteritems():
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134 individual = Individual(column, name)
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135 self.add_individual(individual)
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136
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137 def unwrap_dict(self, wrapped_dict):
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138 decoded_value = self.decode_value(wrapped_dict)
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139 decompressed_value = self.decompress_value(decoded_value)
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140 def _decode_list(data):
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141 rv = []
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142 for item in data:
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143 if isinstance(item, unicode):
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144 item = item.encode('utf-8')
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145 elif isinstance(item, list):
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146 item = _decode_list(item)
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147 elif isinstance(item, dict):
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148 item = _decode_dict(item)
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149 rv.append(item)
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150 return rv
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151 def _decode_dict(data):
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152 rv = {}
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153 for key, value in data.iteritems():
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154 if isinstance(key, unicode):
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155 key = key.encode('utf-8')
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156 if isinstance(value, unicode):
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157 value = value.encode('utf-8')
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158 elif isinstance(value, list):
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159 value = _decode_list(value)
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160 elif isinstance(value, dict):
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161 value = _decode_dict(value)
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162 rv[key] = value
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163 return rv
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164 unwrapped_dict = json.loads(decompressed_value, object_hook=_decode_dict)
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165 return unwrapped_dict
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166
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167 def decode_value(self, value):
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168 try:
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169 return base64.b64decode(value)
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170 except TypeError, message:
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171 print >> sys.stderr, 'base64.b64decode: {0}: {1}'.format(message, value)
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172 sys.exit(1)
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173
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174 def decompress_value(self, value):
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175 try:
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176 return zlib.decompress(value)
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177 except zlib.error, message:
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178 print >> sys.stderr, 'zlib.decompress: {0}'.format(message)
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179 sys.exit(1)
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180
0
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181 def individual_names(self):
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182 for column, individual in self._columns.items():
27
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183 first_token = individual.name.split()[0]
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184 yield first_token
0
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185