Mercurial > repos > iuc > medaka_consensus

annotate convert_VCF_info_fields.py @ 14:b2aae698b9d3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
author iuc
date Thu, 18 Nov 2021 20:01:50 +0000
parents fa11aa8103b2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
1 #!/usr/bin/env python3
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
2
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
3 # Takes in VCF file annotated with medaka tools annotate and converts
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
4 #
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
5 # Usage statement:
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
6 # python convert_VCF_info_fields.py in_vcf.vcf out_vcf.vcf
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
8 # 10/21/2020 - Nathan P. Roach, natproach@gmail.com
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
9
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
10 import re
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
11 import sys
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
12 from collections import OrderedDict
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
13 from math import log10
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
14
11
0413e62b757a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents: 9
diff changeset
15 import scipy.stats
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
16
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
17
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
18 def pval_to_phredqual(pval):
8
6ca28e6144fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 7
diff changeset
19 try:
6ca28e6144fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 7
diff changeset
20 ret = round(-10 * log10(pval))
6ca28e6144fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 7
diff changeset
21 except ValueError:
6ca28e6144fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 7
diff changeset
22 ret = 2147483647 # transform pval of 0.0 to max signed 32 bit int
6ca28e6144fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
iuc
parents: 7
diff changeset
23 return ret
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
24
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
25
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
26 def parseInfoField(info):
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
27 info_fields = info.split(";")
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
28 info_dict = OrderedDict()
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
29 for info_field in info_fields:
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
30 code, val = info_field.split("=")
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
31 info_dict[code] = val
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
32 return info_dict
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
33
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
34
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
35 def annotateVCF(in_vcf_filepath, out_vcf_filepath):
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
36 """Postprocess output of medaka tools annotate.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
37
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
38 Splits multiallelic sites into separate records.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
39 Replaces medaka INFO fields that might represent information of the ref
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
40 and multiple alternate alleles with simple ref, alt allele counterparts.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
41 """
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
42
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
43 in_vcf = open(in_vcf_filepath, "r")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
44 # medaka INFO fields that do not make sense after splitting of
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
45 # multi-allelic records
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
46 # DP will be overwritten with the value of DPSP because medaka tools
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
47 # annotate currently only calculates the latter correctly
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
48 # (https://github.com/nanoporetech/medaka/issues/192).
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
49 # DPS, which is as unreliable as DP, gets skipped and the code
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
50 # calculates the spanning reads equivalent DPSPS instead.
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
51 to_skip = {"SC", "SR", "AR", "DP", "DPSP", "DPS"}
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
52 struct_meta_pat = re.compile("##(.+)=<ID=([^,]+)(,.+)?>")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
53 header_lines = []
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
54 contig_ids = set()
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
55 contig_ids_simple = set()
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
56 # parse the metadata lines of the input VCF and drop:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
57 # - duplicate lines
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
58 # - INFO lines declaring keys we are not going to write
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
59 # - redundant contig information
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
60 while True:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
61 line = in_vcf.readline()
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
62 if line[:2] != "##":
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
63 assert line.startswith("#CHROM")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
64 break
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
65 if line in header_lines:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
66 # the annotate tool may generate lines already written by
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
67 # medaka variant again (example: medaka version line)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
68 continue
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
69 match = struct_meta_pat.match(line)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
70 if match:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
71 match_type, match_id, match_misc = match.groups()
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
72 if match_type == "INFO":
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
73 if match_id == "DPSP":
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
74 line = line.replace("DPSP", "DP")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
75 elif match_id in to_skip:
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
76 continue
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
77 elif match_type == "contig":
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
78 contig_ids.add(match_id)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
79 if not match_misc:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
80 # the annotate tools writes its own contig info,
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
81 # which is redundant with contig info generated by
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
82 # medaka variant, but lacks a length value.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
83 # We don't need the incomplete line.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
84 contig_ids_simple.add(match_id)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
85 continue
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
86 header_lines.append(line)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
87 # Lets check the above assumption about each ID-only contig line
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
88 # having a more complete counterpart.
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
89 assert not (contig_ids_simple - contig_ids)
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
90 header_lines.insert(1, "##convert_VCF_info_fields=0.2\n")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
91 header_lines += [
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
92 '##INFO=<ID=DPSPS,Number=2,Type=Integer,Description="Depth of spanning reads by strand">\n',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
93 '##INFO=<ID=AF,Number=1,Type=Float,Description="Spanning Reads Allele Frequency">\n',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
94 '##INFO=<ID=FAF,Number=1,Type=Float,Description="Forward Spanning Reads Allele Frequency">\n',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
95 '##INFO=<ID=RAF,Number=1,Type=Float,Description="Reverse Spanning Reads Allele Frequency">\n',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
96 '##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias of spanning reads at this position">\n',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
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',
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
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',
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
99 line,
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
100 ]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
101
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
102 with open(out_vcf_filepath, "w") as out_vcf:
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
103 out_vcf.writelines(header_lines)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
104 for line in in_vcf:
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
105 fields = line.split("\t")
7
fbf007713188 "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])
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
107 sr_list = [int(x) for x in info_dict["SR"].split(",")]
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
108 sc_list = [int(x) for x in info_dict["SC"].split(",")]
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
109 if len(sr_list) != len(sc_list):
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
110 print("WARNING - SR and SC are different lengths, " "skipping variant")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
111 print(line.strip()) # Print the line for debugging purposes
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
112 continue
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
113 variant_list = fields[4].split(",")
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
114 dpsp = int(info_dict["DPSP"])
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
115 ref_fwd, ref_rev = 0, 1
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
116 dpspf, dpspr = (int(x) for x in info_dict["AR"].split(","))
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
117 for i in range(0, len(sr_list), 2):
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
118 dpspf += sr_list[i]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
119 dpspr += sr_list[i + 1]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
120 for j, i in enumerate(range(2, len(sr_list), 2)):
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
121 dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
122 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
123 _, p_val = scipy.stats.fisher_exact(dp2x2)
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
124 sb = pval_to_phredqual(p_val)
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
125
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
126 as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
127
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
128 info = []
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
129 for code in info_dict:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
130 if code in to_skip:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
131 continue
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
132 val = info_dict[code]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
133 info.append("%s=%s" % (code, val))
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
134
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
135 info.append("DP=%d" % dpsp)
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
136 info.append("DPSPS=%d,%d" % (dpspf, dpspr))
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
137
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
138 if dpsp == 0:
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
139 info.append("AF=NaN")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
140 else:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
141 af = (dp4[2] + dp4[3]) / dpsp
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
142 info.append("AF=%.6f" % af)
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
143 if dpspf == 0:
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
144 info.append("FAF=NaN")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
145 else:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
146 faf = dp4[2] / dpspf
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
147 info.append("FAF=%.6f" % faf)
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
148 if dpspr == 0:
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
149 info.append("RAF=NaN")
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
150 else:
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
151 raf = dp4[3] / dpspr
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
152 info.append("RAF=%.6f" % raf)
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
153 info.append("SB=%d" % sb)
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
154 info.append("DP4=%d,%d,%d,%d" % dp4)
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
155 info.append("AS=%d,%d,%d,%d" % as_)
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
156 new_info = ";".join(info)
13
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
157 fields[4] = variant_list[j]
fa11aa8103b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 86211daa63a6f39524df8759364795b782324303"
iuc
parents: 11
diff changeset
158 fields[7] = new_info
14
b2aae698b9d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents: 13
diff changeset
159 out_vcf.write("\t".join(fields))
7
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
160 in_vcf.close()
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
161
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
162
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
163 if __name__ == "__main__":
fbf007713188 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents:
diff changeset
164 annotateVCF(sys.argv[1], sys.argv[2])