Mercurial > repos > iuc > medaka_consensus_pipeline

annotate convert_VCF_info_fields.py @ 11:8dfe8a52346f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
author iuc
date Sun, 12 Sep 2021 20:35:45 +0000
parents 1ca4ce7241fd
children 0e9e7fcdd543
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d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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1 #!/usr/bin/env python3
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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2
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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3 # Takes in VCF file annotated with medaka tools annotate and converts
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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4 #
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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5 # Usage statement:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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6 # python convert_VCF_info_fields.py in_vcf.vcf out_vcf.vcf
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d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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8 # 10/21/2020 - Nathan P. Roach, natproach@gmail.com
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9
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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10 import sys
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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11 from collections import OrderedDict
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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12 from math import log10
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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13
10
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
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14 import scipy
1ca4ce7241fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
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15 import scipy.stats
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16
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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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))
57beb8ea55b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
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21 except ValueError:
57beb8ea55b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
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22 ret = 2147483647 # transform pval of 0.0 to max signed 32 bit int
57beb8ea55b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
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23 return ret
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26 def parseInfoField(info):
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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27 info_fields = info.split(';')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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28 info_dict = OrderedDict()
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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29 for info_field in info_fields:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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30 code, val = info_field.split('=')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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31 info_dict[code] = val
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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32 return info_dict
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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34
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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35 def annotateVCF(in_vcf_filepath, out_vcf_filepath):
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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36 in_vcf = open(in_vcf_filepath, 'r')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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37 out_vcf = open(out_vcf_filepath, 'w')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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38 to_skip = set(['SC', 'SR'])
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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39 for i, line in enumerate(in_vcf):
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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40 if i == 1:
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41 out_vcf.write("##convert_VCF_info_fields=0.2\n")
6
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42 if line[0:2] == "##":
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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43 if line[0:11] == "##INFO=<ID=":
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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44 id_ = line[11:].split(',')[0]
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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45 if id_ in to_skip:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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46 continue
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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47 out_vcf.write(line)
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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48 elif line[0] == "#":
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49 out_vcf.write('##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Spanning Reads Allele Frequency By Strand">\n')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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50 out_vcf.write('##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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51 out_vcf.write('##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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52 out_vcf.write('##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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53 out_vcf.write('##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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54 out_vcf.write('##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')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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55 out_vcf.write('##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')
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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56 out_vcf.write(line)
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57 else:
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58 fields = line.split('\t')
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59 info_dict = parseInfoField(fields[7])
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60 sr_list = [int(x) for x in info_dict["SR"].split(',')]
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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61 sc_list = [int(x) for x in info_dict["SC"].split(',')]
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62 if len(sr_list) == len(sc_list):
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63 variant_list = fields[4].split(',')
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64 dpsp = int(info_dict["DPSP"])
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65 ref_fwd, ref_rev = 0, 1
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66 dpspf, dpspr = (int(x) for x in info_dict["AR"].split(','))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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67 for i in range(0, len(sr_list), 2):
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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68 dpspf += sr_list[i]
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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69 dpspr += sr_list[i + 1]
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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70 for j, i in enumerate(range(2, len(sr_list), 2)):
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71 dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
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72 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
10
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73 _, p_val = scipy.stats.fisher_exact(dp2x2)
6
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74 sb = pval_to_phredqual(p_val)
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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75
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76 as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
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77
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78 info = []
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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79 for code in info_dict:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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80 if code in to_skip:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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81 continue
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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82 val = info_dict[code]
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83 info.append("%s=%s" % (code, val))
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84
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85 info.append("DPSPS=%d,%d" % (dpspf, dpspr))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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86
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
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diff changeset
87 if dpsp == 0:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
88 info.append("AF=NaN")
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
89 else:
8
2c72b8c09a70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e0684fe95538cf97b1199ad1072d3da6d1619443"
iuc
parents: 7
diff changeset
90 af = (dp4[2] + dp4[3]) / dpsp
6
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
91 info.append("AF=%.6f" % (af))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
92 if dpspf == 0:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
93 info.append("FAF=NaN")
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
94 else:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
95 faf = dp4[2] / dpspf
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
96 info.append("FAF=%.6f" % (faf))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
97 if dpspr == 0:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
98 info.append("RAF=NaN")
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
99 else:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
100 raf = dp4[3] / dpspr
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
101 info.append("RAF=%.6f" % (raf))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
102 info.append("SB=%d" % (sb))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
103 info.append("DP4=%d,%d,%d,%d" % (dp4))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
104 info.append("AS=%d,%d,%d,%d" % (as_))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
105 new_info = ';'.join(info)
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
106 fields[4] = variant_list[j]
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
107 fields[7] = new_info
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
108 out_vcf.write("%s" % ("\t".join(fields)))
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
109 else:
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
110 print("WARNING - SR and SC are different lengths, skipping variant")
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
111 print(line.strip()) # Print the line for debugging purposes
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
112 in_vcf.close()
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
113 out_vcf.close()
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
114
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
115
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
116 if __name__ == "__main__":
d915879a88bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
117 annotateVCF(sys.argv[1], sys.argv[2])