annotate gff3_rebase.py @ 3:7342f467507b draft

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author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
parents 497c6bb3b717
children ad4b9d7eae6a
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1 #!/usr/bin/env python
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2 import sys
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3 import logging
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4 logging.basicConfig(level=logging.INFO)
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5 import argparse
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6 import copy
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7 from BCBio import GFF
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8 from Bio.SeqFeature import FeatureLocation
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9 log = logging.getLogger(__name__)
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10
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11 __author__ = "Eric Rasche"
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12 __version__ = "0.4.0"
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13 __maintainer__ = "Eric Rasche"
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14 __email__ = "esr@tamu.edu"
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16
3
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17 def feature_lambda(feature_list, test, test_kwargs, subfeatures=True):
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18 """Recursively search through features, testing each with a test function, yielding matches.
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19
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20 GFF3 is a hierachical data structure, so we need to be able to recursively
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21 search through features. E.g. if you're looking for a feature with
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22 ID='bob.42', you can't just do a simple list comprehension with a test
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23 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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24
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25 :type feature_list: list
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26 :param feature_list: an iterable of features
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27
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28 :type test: function reference
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29 :param test: a closure with the method signature (feature, **kwargs) where
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30 the kwargs are those passed in the next argument. This
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31 function should return True or False, True if the feature is
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32 to be yielded as part of the main feature_lambda function, or
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33 False if it is to be ignored. This function CAN mutate the
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34 features passed to it (think "apply").
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35
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36 :type test_kwargs: dictionary
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37 :param test_kwargs: kwargs to pass to your closure when it is called.
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38
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39 :type subfeatures: boolean
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40 :param subfeatures: when a feature is matched, should just that feature be
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41 yielded to the caller, or should the entire sub_feature
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42 tree for that feature be included? subfeatures=True is
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43 useful in cases such as searching for a gene feature,
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44 and wanting to know what RBS/Shine_Dalgarno_sequences
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45 are in the sub_feature tree (which can be accomplished
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46 with two feature_lambda calls). subfeatures=False is
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47 useful in cases when you want to process (and possibly
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48 return) the entire feature tree, such as applying a
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49 qualifier to every single feature.
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50
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51 :rtype: yielded list
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52 :return: Yields a list of matching features.
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53 """
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54 # Either the top level set of [features] or the subfeature attribute
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55 for feature in feature_list:
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56 if test(feature, **test_kwargs):
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57 if not subfeatures:
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58 feature_copy = copy.deepcopy(feature)
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59 feature_copy.sub_features = []
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60 yield feature_copy
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61 else:
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62 yield feature
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63
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64 if hasattr(feature, 'sub_features'):
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65 for x in feature_lambda(feature.sub_features, test, test_kwargs, subfeatures=subfeatures):
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66 yield x
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67
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68
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69 def feature_test_qual_value(feature, **kwargs):
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70 """Test qualifier values.
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71
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72 For every feature, check that at least one value in
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73 feature.quailfiers(kwargs['qualifier']) is in kwargs['attribute_list']
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74 """
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75 for attribute_value in feature.qualifiers.get(kwargs['qualifier'], []):
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76 if attribute_value in kwargs['attribute_list']:
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77 return True
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78 return False
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79
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80
1
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81 def __get_features(child, interpro=False):
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82 child_features = {}
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83 for rec in GFF.parse(child):
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84 for feature in rec.features:
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85 parent_feature_id = rec.id
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86 if interpro:
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87 if feature.type == 'polypeptide':
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88 continue
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89 if '_' in parent_feature_id:
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90 parent_feature_id = parent_feature_id[parent_feature_id.index('_') + 1:]
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91
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92 try:
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93 child_features[parent_feature_id].append(feature)
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94 except KeyError:
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95 child_features[parent_feature_id] = [feature]
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96 return child_features
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97
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98
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99 def __update_feature_location(feature, parent, protein2dna):
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100 start = feature.location.start
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101 end = feature.location.end
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102 if protein2dna:
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103 start *= 3
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104 end *= 3
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105
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106 if parent.location.strand >= 0:
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107 ns = parent.location.start + start
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108 ne = parent.location.start + end
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109 st = +1
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110 else:
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111 ns = parent.location.end - end
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112 ne = parent.location.end - start
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113 st = -1
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114
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115 # Don't let start/stops be less than zero. It's technically valid for them
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116 # to be (at least in the model I'm working with) but it causes numerous
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117 # issues.
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118 #
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119 # Instead, we'll replace with %3 to try and keep it in the same reading
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120 # frame that it should be in.
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121 if ns < 0:
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122 ns %= 3
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123 if ne < 0:
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124 ne %= 3
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125
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126 feature.location = FeatureLocation(ns, ne, strand=st)
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127
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128 if hasattr(feature, 'sub_features'):
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129 for subfeature in feature.sub_features:
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130 __update_feature_location(subfeature, parent, protein2dna)
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131
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132
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133 def rebase(parent, child, interpro=False, protein2dna=False):
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134 child_features = __get_features(child, interpro=interpro)
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135
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136 for rec in GFF.parse(parent):
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137 replacement_features = []
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138 for feature in feature_lambda(
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139 rec.features,
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140 feature_test_qual_value,
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141 {
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142 'qualifier': 'ID',
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143 'attribute_list': child_features.keys(),
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144 },
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145 subfeatures=False):
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146
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147 new_subfeatures = child_features[feature.id]
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148 fixed_subfeatures = []
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149 for x in new_subfeatures:
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150 # Then update the location of the actual feature
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151 __update_feature_location(x, feature, protein2dna)
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152
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153 if interpro:
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154 for y in ('status', 'Target'):
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155 try:
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156 del x.qualifiers[y]
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157 except:
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158 pass
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159
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160 fixed_subfeatures.append(x)
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161 replacement_features.extend(fixed_subfeatures)
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162 # We do this so we don't include the original set of features that we
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163 # were rebasing against in our result.
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164 rec.features = replacement_features
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165 rec.annotations = {}
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166 GFF.write([rec], sys.stdout)
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167
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168
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169 if __name__ == '__main__':
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170 parser = argparse.ArgumentParser(description='rebase gff3 features against parent locations', epilog="")
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171 parser.add_argument('parent', type=file, help='Parent GFF3 annotations')
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172 parser.add_argument('child', help='Child GFF3 annotations to rebase against parent')
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173 parser.add_argument('--interpro', action='store_true',
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174 help='Interpro specific modifications')
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175 parser.add_argument('--protein2dna', action='store_true',
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176 help='Map protein translated results to original DNA data')
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177 args = parser.parse_args()
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178 rebase(**vars(args))