Mercurial > repos > iuc > medaka_consensus

annotate convert_VCF_info_fields.py @ 19:6cd17fecb4ef draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:57:32 +0000
parents 95a9a77b9e47
children
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1 #!/usr/bin/env python3
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3 # Takes in VCF file annotated with medaka tools annotate and converts
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4 #
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5 # Usage statement:
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6 # python convert_VCF_info_fields.py in_vcf.vcf out_vcf.vcf
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8 # 10/21/2020 - Nathan P. Roach, natproach@gmail.com
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10 import re
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11 import sys
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12 from collections import OrderedDict
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13 from math import log10
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15 import scipy.stats
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18 def pval_to_phredqual(pval):
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19 try:
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20 ret = round(-10 * log10(pval))
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21 except ValueError:
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22 ret = 2147483647 # transform pval of 0.0 to max signed 32 bit int
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23 return ret
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26 def parseInfoField(info):
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27 info_fields = info.split(";")
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28 info_dict = OrderedDict()
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29 for info_field in info_fields:
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30 code, val = info_field.split("=")
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31 info_dict[code] = val
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32 return info_dict
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35 def annotateVCF(in_vcf_filepath, out_vcf_filepath):
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36 """Postprocess output of medaka tools annotate.
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38 Splits multiallelic sites into separate records.
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39 Replaces medaka INFO fields that might represent information of the ref
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40 and multiple alternate alleles with simple ref, alt allele counterparts.
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41 """
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42
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43 in_vcf = open(in_vcf_filepath, "r")
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44 # medaka INFO fields that do not make sense after splitting of
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45 # multi-allelic records
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46 # DP will be overwritten with the value of DPSP because medaka tools
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47 # annotate currently only calculates the latter correctly
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48 # (https://github.com/nanoporetech/medaka/issues/192).
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49 # DPS, which is as unreliable as DP, gets skipped and the code
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50 # calculates the spanning reads equivalent DPSPS instead.
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51 to_skip = {"SC", "SR", "AR", "DP", "DPSP", "DPS"}
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52 struct_meta_pat = re.compile("##(.+)=<ID=([^,]+)(,.+)?>")
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53 header_lines = []
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54 contig_ids = set()
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55 contig_ids_simple = set()
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56 # parse the metadata lines of the input VCF and drop:
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57 # - duplicate lines
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58 # - INFO lines declaring keys we are not going to write
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59 # - redundant contig information
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60 while True:
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61 line = in_vcf.readline()
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62 if line[:2] != "##":
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63 assert line.startswith("#CHROM")
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64 break
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65 if line in header_lines:
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66 # the annotate tool may generate lines already written by
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67 # medaka variant again (example: medaka version line)
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68 continue
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69 match = struct_meta_pat.match(line)
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70 if match:
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71 match_type, match_id, match_misc = match.groups()
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72 if match_type == "INFO":
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73 if match_id == "DPSP":
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74 line = line.replace("DPSP", "DP")
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75 elif match_id in to_skip:
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76 continue
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77 elif match_type == "contig":
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78 contig_ids.add(match_id)
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79 if not match_misc:
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80 # the annotate tools writes its own contig info,
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81 # which is redundant with contig info generated by
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82 # medaka variant, but lacks a length value.
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83 # We don't need the incomplete line.
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84 contig_ids_simple.add(match_id)
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85 continue
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86 header_lines.append(line)
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87 # Lets check the above assumption about each ID-only contig line
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88 # having a more complete counterpart.
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iuc
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89 assert not (contig_ids_simple - contig_ids)
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iuc
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90 header_lines.insert(1, "##convert_VCF_info_fields=0.2\n")
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iuc
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91 header_lines += [
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iuc
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92 '##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Depth of spanning reads by strand">\n',
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iuc
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93 '##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n',
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iuc
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94 '##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n',
a5b6aed7e6d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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95 '##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n',
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iuc
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96 '##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n',
a5b6aed7e6d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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97 '##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases in spanning reads">\n',
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iuc
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98 '##INFO=<ID=AS,Number=4,Type=Integer,Description="Total alignment score to ref and alt allele of spanning reads by strand (ref fwd, ref rev, alt fwd, alt rev) aligned with parasail match 5, mismatch -4, open 5, extend 3">\n',
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iuc
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diff changeset
99 line,
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100 ]
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101
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102 with open(out_vcf_filepath, "w") as out_vcf:
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iuc
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103 out_vcf.writelines(header_lines)
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iuc
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104 for line in in_vcf:
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105 fields = line.split("\t")
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106 info_dict = parseInfoField(fields[7])
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107 sr_list = [int(x) for x in info_dict["SR"].split(",")]
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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108 sc_list = [int(x) for x in info_dict["SC"].split(",")]
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109 if len(sr_list) != len(sc_list):
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iuc
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110 print("WARNING - SR and SC are different lengths, " "skipping variant")
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iuc
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111 print(line.strip()) # Print the line for debugging purposes
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112 continue
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113 variant_list = fields[4].split(",")
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114 dpsp = int(info_dict["DPSP"])
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115 ref_fwd, ref_rev = 0, 1
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116 dpspf, dpspr = (int(x) for x in info_dict["AR"].split(","))
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117 for i in range(0, len(sr_list), 2):
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iuc
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118 dpspf += sr_list[i]
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119 dpspr += sr_list[i + 1]
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120 for j, i in enumerate(range(2, len(sr_list), 2)):
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121 dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
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122 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
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123 _, p_val = scipy.stats.fisher_exact(dp2x2)
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124 sb = pval_to_phredqual(p_val)
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125
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126 as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
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127
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128 info = []
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129 for code in info_dict:
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130 if code in to_skip:
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131 continue
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132 val = info_dict[code]
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133 info.append("%s=%s" % (code, val))
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134
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135 info.append("DP=%d" % dpsp)
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136 info.append("DPSPS=%d,%d" % (dpspf, dpspr))
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137
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138 if dpsp == 0:
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139 info.append("AF=NaN")
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140 else:
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141 af = (dp4[2] + dp4[3]) / dpsp
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142 info.append("AF=%.6f" % af)
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143 if dpspf == 0:
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144 info.append("FAF=NaN")
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145 else:
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146 faf = dp4[2] / dpspf
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147 info.append("FAF=%.6f" % faf)
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148 if dpspr == 0:
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149 info.append("RAF=NaN")
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iuc
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150 else:
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151 raf = dp4[3] / dpspr
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diff changeset
152 info.append("RAF=%.6f" % raf)
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153 info.append("SB=%d" % sb)
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154 info.append("DP4=%d,%d,%d,%d" % dp4)
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iuc
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diff changeset
155 info.append("AS=%d,%d,%d,%d" % as_)
95a9a77b9e47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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156 new_info = ";".join(info)
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diff changeset
157 fields[4] = variant_list[j]
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158 fields[7] = new_info
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diff changeset
159 out_vcf.write("\t".join(fields))
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160 in_vcf.close()
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161
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162
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163 if __name__ == "__main__":
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diff changeset
164 annotateVCF(sys.argv[1], sys.argv[2])