Mercurial > repos > cpt > cpt_gff_rebase

annotate gff3_rebase.py @ 1:4f4b413056f6 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:44:12 +0000
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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 import argparse
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5 from gff3 import feature_lambda, feature_test_qual_value
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6 from CPT_GFFParser import gffParse, gffWrite
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7 from Bio.SeqFeature import FeatureLocation
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8
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9 log = logging.getLogger(__name__)
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10 logging.basicConfig(level=logging.INFO)
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11
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12
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13 def __get_features(child, interpro=False):
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14 child_features = {}
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15 for rec in gffParse(child):
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16 log.info("Parsing %s", rec.id)
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17 # Only top level
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18 for feature in rec.features:
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19 # Get the record id as parent_feature_id (since this is how it will be during remapping)
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20 parent_feature_id = rec.id
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21 # If it's an interpro specific gff3 file
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22 if interpro:
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23 # Then we ignore polypeptide features as they're useless
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24 if feature.type == "polypeptide":
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25 continue
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26
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27 try:
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28 child_features[parent_feature_id].append(feature)
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29 except KeyError:
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30 child_features[parent_feature_id] = [feature]
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31 # Keep a list of feature objects keyed by parent record id
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32 return child_features
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33
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34
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35 def __update_feature_location(feature, parent, protein2dna):
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36 start = feature.location.start
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37 end = feature.location.end
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38 if protein2dna:
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39 start *= 3
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40 end *= 3
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41
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42 if parent.location.strand >= 0:
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43 ns = parent.location.start + start
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44 ne = parent.location.start + end
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45 st = +1
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46 else:
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47 ns = parent.location.end - end
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48 ne = parent.location.end - start
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49 st = -1
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50
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51 # Don't let start/stops be less than zero.
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52 #
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53 # Instead, we'll replace with %3 to try and keep it in the same reading
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54 # frame that it should be in.
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55
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56 if ns < 0:
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57 ns %= 3
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58 if ne < 0:
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59 ne %= 3
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60
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61 feature.location = FeatureLocation(ns, ne, strand=st)
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62
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63 if hasattr(feature, "sub_features"):
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64 for subfeature in feature.sub_features:
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65 __update_feature_location(subfeature, parent, protein2dna)
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66
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67
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68 def rebase(parent, child, interpro=False, protein2dna=False, map_by="ID"):
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69 # get all of the features we will be re-mapping in a dictionary, keyed by parent feature ID
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70 child_features = __get_features(child, interpro=interpro)
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71
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72 for rec in gffParse(parent):
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73 replacement_features = []
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74 # Horrifically slow I believe
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75 for feature in feature_lambda(
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76 rec.features,
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77 # Filter features in the parent genome by those that are
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78 # "interesting", i.e. have results in child_features array.
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79 # Probably an unnecessary optimisation.
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80 feature_test_qual_value,
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81 {"qualifier": map_by, "attribute_list": child_features.keys()},
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82 subfeatures=False,
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83 ):
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84
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85 # Features which will be re-mapped
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86 to_remap = child_features[feature.id]
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87
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88 fixed_features = []
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89 for x in to_remap:
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90 # Then update the location of the actual feature
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91 __update_feature_location(x, feature, protein2dna)
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92
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93 if interpro:
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94 for y in ("status", "Target"):
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95 try:
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96 del x.qualifiers[y]
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97 except:
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98 pass
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99
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100 fixed_features.append(x)
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101 replacement_features.extend(fixed_features)
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102 # We do this so we don't include the original set of features that we
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103 # were rebasing against in our result.
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104 rec.features = replacement_features
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105 rec.annotations = {}
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106 gffWrite([rec], sys.stdout)
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107
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108
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109 if __name__ == "__main__":
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110 parser = argparse.ArgumentParser(
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111 description="rebase gff3 features against parent locations", epilog=""
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112 )
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113 parser.add_argument(
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114 "parent", type=argparse.FileType("r"), help="Parent GFF3 annotations"
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115 )
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116 parser.add_argument(
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117 "child",
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118 type=argparse.FileType("r"),
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119 help="Child GFF3 annotations to rebase against parent",
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120 )
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121 parser.add_argument(
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122 "--interpro", action="store_true", help="Interpro specific modifications"
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123 )
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124 parser.add_argument(
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125 "--protein2dna",
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126 action="store_true",
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127 help="Map protein translated results to original DNA data",
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128 )
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129 parser.add_argument("--map_by", help="Map by key", default="ID")
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130 args = parser.parse_args()
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131 rebase(**vars(args))