Mercurial > repos > iuc > medaka_variant_pipeline

annotate convert_VCF_info_fields.py @ 12:597407d61386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
author iuc
date Fri, 17 Sep 2021 20:22:27 +0000
parents 7623e5888be9
children 3fbefde449bc
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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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9
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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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89 assert not (contig_ids_simple - contig_ids)
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90 header_lines.insert(1, '##convert_VCF_info_fields=0.2\n')
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91 header_lines += [
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92 '##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Depth of spanning reads by strand">\n',
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parents: 10
diff changeset
93 '##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
94 '##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
95 '##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
96 '##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
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',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
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',
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
99 line
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
100 ]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
101
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
102 with open(out_vcf_filepath, 'w') as out_vcf:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
103 out_vcf.writelines(header_lines)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
104 for line in in_vcf:
6
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
105 fields = line.split('\t')
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
106 info_dict = parseInfoField(fields[7])
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
107 sr_list = [int(x) for x in info_dict["SR"].split(',')]
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
108 sc_list = [int(x) for x in info_dict["SC"].split(',')]
12
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
109 if len(sr_list) != len(sc_list):
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
110 print(
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
111 'WARNING - SR and SC are different lengths, '
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
112 'skipping variant'
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
113 )
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
114 print(line.strip()) # Print the line for debugging purposes
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
115 continue
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
116 variant_list = fields[4].split(',')
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
117 dpsp = int(info_dict['DPSP'])
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
118 ref_fwd, ref_rev = 0, 1
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
119 dpspf, dpspr = (int(x) for x in info_dict['AR'].split(','))
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
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120 for i in range(0, len(sr_list), 2):
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
121 dpspf += sr_list[i]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
122 dpspr += sr_list[i + 1]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
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123 for j, i in enumerate(range(2, len(sr_list), 2)):
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
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124 dp4 = (
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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125 sr_list[ref_fwd],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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126 sr_list[ref_rev],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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127 sr_list[i],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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128 sr_list[i + 1]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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129 )
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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130 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
131 _, p_val = scipy.stats.fisher_exact(dp2x2)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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132 sb = pval_to_phredqual(p_val)
6
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133
12
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iuc
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diff changeset
134 as_ = (
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
135 sc_list[ref_fwd],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
136 sc_list[ref_rev],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
137 sc_list[i],
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
138 sc_list[i + 1]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
139 )
6
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
140
12
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
141 info = []
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
142 for code in info_dict:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
143 if code in to_skip:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
144 continue
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
145 val = info_dict[code]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
146 info.append("%s=%s" % (code, val))
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
147
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
148 info.append('DP=%d' % dpsp)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
149 info.append('DPSPS=%d,%d' % (dpspf, dpspr))
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
150
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
151 if dpsp == 0:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
152 info.append('AF=NaN')
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
153 else:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
154 af = (dp4[2] + dp4[3]) / dpsp
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
155 info.append('AF=%.6f' % af)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
156 if dpspf == 0:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
157 info.append('FAF=NaN')
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
158 else:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
159 faf = dp4[2] / dpspf
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
160 info.append('FAF=%.6f' % faf)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
161 if dpspr == 0:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
162 info.append('RAF=NaN')
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
163 else:
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
164 raf = dp4[3] / dpspr
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
165 info.append('RAF=%.6f' % raf)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
166 info.append('SB=%d' % sb)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
167 info.append('DP4=%d,%d,%d,%d' % dp4)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
168 info.append('AS=%d,%d,%d,%d' % as_)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
169 new_info = ';'.join(info)
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 10
diff changeset
170 fields[4] = variant_list[j]
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
171 fields[7] = new_info
597407d61386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
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diff changeset
172 out_vcf.write('\t'.join(fields))
6
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
173 in_vcf.close()
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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174
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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parents:
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175
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
176 if __name__ == "__main__":
ea1833858055 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
177 annotateVCF(sys.argv[1], sys.argv[2])