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annotate gff3.py @ 3:4451729a0a3b draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:58 +0000
parents ae5f291c788d
children
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1 import copy
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2 import logging
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3
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4 log = logging.getLogger()
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5 log.setLevel(logging.WARN)
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6
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7
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8 def feature_lambda(
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9 feature_list,
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10 test,
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11 test_kwargs,
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12 subfeatures=True,
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13 parent=None,
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14 invert=False,
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15 recurse=True,
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16 ):
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17 """Recursively search through features, testing each with a test function, yielding matches.
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18
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19 GFF3 is a hierachical data structure, so we need to be able to recursively
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20 search through features. E.g. if you're looking for a feature with
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21 ID='bob.42', you can't just do a simple list comprehension with a test
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22 case. You don't know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.
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23
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24 :type feature_list: list
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25 :param feature_list: an iterable of features
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26
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27 :type test: function reference
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28 :param test: a closure with the method signature (feature, **kwargs) where
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29 the kwargs are those passed in the next argument. This
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30 function should return True or False, True if the feature is
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31 to be yielded as part of the main feature_lambda function, or
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32 False if it is to be ignored. This function CAN mutate the
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33 features passed to it (think "apply").
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34
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35 :type test_kwargs: dictionary
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36 :param test_kwargs: kwargs to pass to your closure when it is called.
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37
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38 :type subfeatures: boolean
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39 :param subfeatures: when a feature is matched, should just that feature be
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40 yielded to the caller, or should the entire sub_feature
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41 tree for that feature be included? subfeatures=True is
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42 useful in cases such as searching for a gene feature,
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43 and wanting to know what RBS/Shine_Dalgarno_sequences
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44 are in the sub_feature tree (which can be accomplished
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45 with two feature_lambda calls). subfeatures=False is
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46 useful in cases when you want to process (and possibly
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47 return) the entire feature tree, such as applying a
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48 qualifier to every single feature.
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49
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50 :type invert: boolean
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51 :param invert: Negate/invert the result of the filter.
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52
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53 :rtype: yielded list
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54 :return: Yields a list of matching features.
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55 """
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56 # Either the top level set of [features] or the subfeature attribute
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57 for feature in feature_list:
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58 feature._parent = parent
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59 if not parent:
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60 # Set to self so we cannot go above root.
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61 feature._parent = feature
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62 test_result = test(feature, **test_kwargs)
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63 # if (not invert and test_result) or (invert and not test_result):
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64 if invert ^ test_result:
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65 if not subfeatures:
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66 feature_copy = copy.deepcopy(feature)
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67 feature_copy.sub_features = list()
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68 yield feature_copy
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69 else:
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70 yield feature
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71
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72 if recurse and hasattr(feature, "sub_features"):
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73 for x in feature_lambda(
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74 feature.sub_features,
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75 test,
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76 test_kwargs,
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77 subfeatures=subfeatures,
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78 parent=feature,
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79 invert=invert,
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80 recurse=recurse,
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81 ):
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82 yield x
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83
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84
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85 def fetchParent(feature):
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86 if not hasattr(feature, "_parent") or feature._parent is None:
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87 return feature
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88 else:
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89 return fetchParent(feature._parent)
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90
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91
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92 def feature_test_true(feature, **kwargs):
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93 return True
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94
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95
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96 def feature_test_type(feature, **kwargs):
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97 if "type" in kwargs:
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98 return str(feature.type).upper() == str(kwargs["type"]).upper()
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99 elif "types" in kwargs:
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100 for x in kwargs["types"]:
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101 if str(feature.type).upper() == str(x).upper():
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102 return True
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103 return False
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104 raise Exception("Incorrect feature_test_type call, need type or types")
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105
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106
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107 def feature_test_qual_value(feature, **kwargs):
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108 """Test qualifier values.
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109
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110 For every feature, check that at least one value in
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111 feature.quailfiers(kwargs['qualifier']) is in kwargs['attribute_list']
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112 """
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113 if isinstance(kwargs["qualifier"], list):
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114 for qualifier in kwargs["qualifier"]:
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115 for attribute_value in feature.qualifiers.get(qualifier, []):
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116 if attribute_value in kwargs["attribute_list"]:
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117 return True
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118 else:
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119 for attribute_value in feature.qualifiers.get(kwargs["qualifier"], []):
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120 if attribute_value in kwargs["attribute_list"]:
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121 return True
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122 return False
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123
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124
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125 def feature_test_location(feature, **kwargs):
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126 if "strand" in kwargs:
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127 if feature.location.strand != kwargs["strand"]:
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128 return False
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129
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130 return feature.location.start <= kwargs["loc"] <= feature.location.end
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131
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132
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133 def feature_test_quals(feature, **kwargs):
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134 """
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135 Example::
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136
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137 a = Feature(qualifiers={'Note': ['Some notes', 'Aasdf']})
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138
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139 # Check if a contains a Note
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140 feature_test_quals(a, {'Note': None}) # Returns True
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141 feature_test_quals(a, {'Product': None}) # Returns False
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142
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143 # Check if a contains a note with specific value
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144 feature_test_quals(a, {'Note': ['ome']}) # Returns True
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145
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146 # Check if a contains a note with specific value
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147 feature_test_quals(a, {'Note': ['other']}) # Returns False
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148 """
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149 for key in kwargs:
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150 if key not in feature.qualifiers:
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151 return False
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152
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153 # Key is present, no value specified
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154 if kwargs[key] is None:
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155 return True
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156
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157 # Otherwise there is a key value we're looking for.
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158 # so we make a list of matches
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159 matches = []
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160 # And check all of the feature qualifier valuse
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161 for value in feature.qualifiers[key]:
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162 # For that kwargs[key] value
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163 for x in kwargs[key]:
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164 matches.append(x in value)
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165
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166 # If none matched, then we return false.
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167 if not any(matches):
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168 return False
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169
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170 return True
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171
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172
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173 def feature_test_contains(feature, **kwargs):
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174 if "index" in kwargs:
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175 return feature.location.start < kwargs["index"] < feature.location.end
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176 elif "range" in kwargs:
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177 return (
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178 feature.location.start < kwargs["range"]["start"] < feature.location.end
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179 and feature.location.start < kwargs["range"]["end"] < feature.location.end
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180 )
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181 else:
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182 raise RuntimeError("Must use index or range keyword")
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183
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184
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185 def get_id(feature=None, parent_prefix=None):
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186 result = ""
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187 if parent_prefix is not None:
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188 result += parent_prefix + "|"
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189 if "locus_tag" in feature.qualifiers:
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190 result += feature.qualifiers["locus_tag"][0]
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191 elif "gene" in feature.qualifiers:
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192 result += feature.qualifiers["gene"][0]
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193 elif "Gene" in feature.qualifiers:
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194 result += feature.qualifiers["Gene"][0]
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195 elif "product" in feature.qualifiers:
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196 result += feature.qualifiers["product"][0]
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197 elif "Product" in feature.qualifiers:
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198 result += feature.qualifiers["Product"][0]
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199 elif "Name" in feature.qualifiers:
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200 result += feature.qualifiers["Name"][0]
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201 else:
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202 return feature.id
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203 # Leaving in case bad things happen.
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204 # result += '%s_%s_%s_%s' % (
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205 # feature.id,
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206 # feature.location.start,
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207 # feature.location.end,
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208 # feature.location.strand
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209 # )
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210 return result
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211
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212
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213 def get_gff3_id(gene):
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214 return gene.qualifiers.get("Name", [gene.id])[0]
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215
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216
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217 def ensure_location_in_bounds(start=0, end=0, parent_length=0):
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218 # This prevents frameshift errors
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219 while start < 0:
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220 start += 3
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221 while end < 0:
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222 end += 3
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223 while start > parent_length:
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224 start -= 3
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225 while end > parent_length:
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226 end -= 3
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227 return (start, end)
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228
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229
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230 def coding_genes(feature_list):
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231 for x in genes(feature_list):
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232 if (
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233 len(
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234 list(
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235 feature_lambda(
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236 x.sub_features,
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237 feature_test_type,
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238 {"type": "CDS"},
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239 subfeatures=False,
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240 )
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241 )
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242 )
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243 > 0
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244 ):
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245 yield x
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246
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247
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248 def genes(feature_list, feature_type="gene", sort=False):
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249 """
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250 Simple filter to extract gene features from the feature set.
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251 """
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252
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253 if not sort:
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254 for x in feature_lambda(
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255 feature_list, feature_test_type, {"type": feature_type}, subfeatures=True
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256 ):
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257 yield x
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258 else:
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259 data = list(genes(feature_list, feature_type=feature_type, sort=False))
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260 data = sorted(data, key=lambda feature: feature.location.start)
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261 for x in data:
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262 yield x
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263
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264
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265 def wa_unified_product_name(feature):
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266 """
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267 Try and figure out a name. We gave conflicting instructions, so
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268 this isn't as trivial as it should be. Sometimes it will be in
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269 'product' or 'Product', othertimes in 'Name'
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270 """
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271 # Manually applied tags.
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272 protein_product = feature.qualifiers.get(
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273 "product", feature.qualifiers.get("Product", [None])
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274 )[0]
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275
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276 # If neither of those are available ...
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277 if protein_product is None:
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278 # And there's a name...
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279 if "Name" in feature.qualifiers:
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280 if not is_uuid(feature.qualifiers["Name"][0]):
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281 protein_product = feature.qualifiers["Name"][0]
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282
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283 return protein_product
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284
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285
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286 def is_uuid(name):
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287 return name.count("-") == 4 and len(name) == 36
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288
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289
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290 def get_rbs_from(gene):
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291 # Normal RBS annotation types
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292 rbs_rbs = list(
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293 feature_lambda(
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294 gene.sub_features, feature_test_type, {"type": "RBS"}, subfeatures=False
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295 )
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296 )
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297 rbs_sds = list(
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298 feature_lambda(
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299 gene.sub_features,
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300 feature_test_type,
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301 {"type": "Shine_Dalgarno_sequence"},
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302 subfeatures=False,
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303 )
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304 )
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305 # Fraking apollo
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306 apollo_exons = list(
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307 feature_lambda(
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308 gene.sub_features, feature_test_type, {"type": "exon"}, subfeatures=False
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309 )
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310 )
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311 apollo_exons = [x for x in apollo_exons if len(x) < 10]
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312 # These are more NCBI's style
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313 regulatory_elements = list(
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314 feature_lambda(
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315 gene.sub_features,
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316 feature_test_type,
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317 {"type": "regulatory"},
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318 subfeatures=False,
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319 )
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320 )
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321 rbs_regulatory = list(
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322 feature_lambda(
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323 regulatory_elements,
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324 feature_test_quals,
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325 {"regulatory_class": ["ribosome_binding_site"]},
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326 subfeatures=False,
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327 )
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328 )
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329 # Here's hoping you find just one ;)
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330 return rbs_rbs + rbs_sds + rbs_regulatory + apollo_exons
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331
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332
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333 def nice_name(record):
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334 """
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335 get the real name rather than NCBI IDs and so on. If fails, will return record.id
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336 """
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337 name = record.id
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338 likely_parental_contig = list(genes(record.features, feature_type="contig"))
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339 if len(likely_parental_contig) == 1:
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340 name = likely_parental_contig[0].qualifiers.get("organism", [name])[0]
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341 return name
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342
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343
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344 def fsort(it):
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345 for i in sorted(it, key=lambda x: int(x.location.start)):
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346 yield i