Mercurial > repos > cpt > cpt_gff_rebase
annotate gff3_rebase.py @ 2:d0b52c1d6b25 draft default tip
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author | cpt |
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date | Fri, 05 Jan 2024 05:52:31 +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)) |