Mercurial > repos > cpt > cpt_genome_editor

annotate genome_editor.py @ 5:0e8079ac24f8 draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:51:54 +0000
parents 134bb2d7cdfd
children
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1 #!/usr/bin/env python
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2 import logging
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3 import copy
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4 import argparse
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5 import tsv
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6 from Bio import SeqIO
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7 from Bio.Seq import Seq
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8 from Bio.SeqFeature import FeatureLocation
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9 from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature, convertSeqRec
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10 from gff3 import feature_lambda, feature_test_contains
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11
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12 logging.basicConfig(level=logging.INFO)
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13 log = logging.getLogger(__name__)
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14
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15
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16 def mutate(gff3, fasta, changes, customSeqs, new_id):
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17 # Change Language
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18 # - we can only accept ONE genome as an input. (TODO: support multiple?)
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19 # - we can only build ONE genome as an output. (TODO: support multiple?)
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20 # - must allow selection of various regions
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21 # '1,1000,+ 40,100,- custom_seq_1'
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22 try:
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23 custom_seqs = SeqIO.to_dict(SeqIO.parse(customSeqs, "fasta"))
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24 except:
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25 custom_seqs = {}
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26 seq_dict = SeqIO.to_dict(SeqIO.parse(fasta, "fasta"))
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27 # Pull first and onl record
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28 rec = list(gffParse(gff3, base_dict=seq_dict))[0]
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29 # Create a "clean" record
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30 new_record = copy.deepcopy(rec)
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31 new_record.id = new_id
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32 new_record.seq = Seq("")
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33 new_record.features = []
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34 new_record.annotations = {}
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35 # Process changes.
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36 chain = []
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37 topFeats = {}
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38 covered = 0
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39 for feat in rec.features:
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40 if "ID" in feat.qualifiers.keys():
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41 topFeats[feat.qualifiers["ID"][0]] = feat.location.start
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42 for change in changes:
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43 if "," in change:
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44 (start, end, strand) = change.split(",")
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45 start = int(start) - 1
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46 end = int(end)
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47
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48 # Make any complaints
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49 broken_feature_start = list(
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50 feature_lambda(
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51 rec.features,
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52 feature_test_contains,
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53 {"index": start},
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54 subfeatures=False,
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55 )
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56 )
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57 if len(broken_feature_start) > 0:
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58 pass
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59 # log.info("DANGER: Start index chosen (%s) is in the middle of a feature (%s %s). This feature will disappear from the output", start, broken_feature_start[0].id, broken_feature_start[0].location)
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60 broken_feature_end = list(
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61 feature_lambda(
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62 rec.features,
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63 feature_test_contains,
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64 {"index": end},
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65 subfeatures=False,
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66 )
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67 )
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68 if len(broken_feature_end) > 0:
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69 pass
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70 # log.info("DANGER: End index chosen (%s) is in the middle of a feature (%s %s). This feature will disappear from the output", end, broken_feature_end[0].id, broken_feature_end[0].location)
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71
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72 # Ok, fetch features
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73 if strand == "+":
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74 tmp_req = rec[start:end]
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75 else:
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76 tmp_req = rec[start:end].reverse_complement(
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77 id=True,
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78 name=True,
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79 description=True,
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80 features=True,
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81 annotations=True,
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82 letter_annotations=True,
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83 dbxrefs=True,
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84 )
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85 tmp_req = convertSeqRec(tmp_req)[0]
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86
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87 def update_location(feature, shiftS):
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88 feature.location = FeatureLocation(
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89 feature.location.start + shiftS,
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90 feature.location.end + shiftS,
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91 feature.strand,
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92 )
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93 for i in feature.sub_features:
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94 i = update_location(i, shiftS)
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95 return feature
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96
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97 # for feature in tmp_req.features:
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98
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99 chain.append(
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100 [
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101 rec.id,
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102 start + 1,
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103 end,
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104 strand,
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105 new_record.id,
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106 len(new_record) + 1,
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107 len(new_record) + (end - start),
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108 "+",
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109 ]
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110 )
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111
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112 covered += len(new_record.seq)
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113 print(covered)
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114 new_record.seq += tmp_req.seq
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115 # NB: THIS MUST USE BIOPYTHON 1.67. 1.68 Removes access to
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116 # subfeatures, which means you will only get top-level features.
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117 startInd = len(new_record.features)
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118 new_record.features += tmp_req.features
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119
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120 for i in new_record.features[startInd:]:
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121 i.location = FeatureLocation(
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122 i.location.start + covered,
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123 i.location.end + covered,
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124 i.location.strand,
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125 )
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126 if "ID" not in i.qualifiers.keys():
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127 continue
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128 diffS = i.location.start - topFeats[i.qualifiers["ID"][0]]
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129 subFeats = i.sub_features
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130 for j in subFeats:
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131 j = update_location(j, diffS)
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132 else:
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133 new_record.seq += custom_seqs[change].seq
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134 yield new_record, chain
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135
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136
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137 if __name__ == "__main__":
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138 parser = argparse.ArgumentParser()
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139 parser.add_argument("fasta", type=argparse.FileType("r"), help="Sequence")
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140 parser.add_argument("gff3", type=argparse.FileType("r"), help="Annotations")
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141 parser.add_argument("new_id", help="Append to ID", default="_v2")
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142 parser.add_argument(
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143 "--out_fasta",
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144 type=argparse.FileType("w"),
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145 help="Output fasta",
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146 default="out.fa",
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147 )
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148 parser.add_argument(
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149 "--out_gff3",
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150 type=argparse.FileType("w"),
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151 help="Output gff3",
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152 default="out.gff3",
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153 )
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154 parser.add_argument(
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155 "--out_simpleChain",
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156 type=argparse.FileType("w"),
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157 help="Output simple chain (i.e. not a real UCSC chain file)",
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158 default="out.chain",
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159 )
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160 parser.add_argument("--changes", nargs="+")
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161 parser.add_argument("--customSeqs", type=argparse.FileType("r"))
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162 args = parser.parse_args()
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163
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164 for rec, chain in mutate(
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165 args.gff3, args.fasta, args.changes, args.customSeqs, args.new_id
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166 ):
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167 # TODO: Check that this appends and doesn't overwirte
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168 gffWrite([rec], args.out_gff3)
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169 SeqIO.write([rec], args.out_fasta, "fasta")
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170 tsv.dump(chain, args.out_simpleChain)