Mercurial > repos > iuc > ivar_consensus

annotate ivar_variants_to_vcf.py @ 16:17f911830a8c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
author iuc
date Tue, 27 Jun 2023 17:14:55 +0000
parents 3bc2ef3d4a17
children
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3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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1 #!/usr/bin/env python
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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2 import argparse
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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3 import errno
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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4 import os
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5 import re
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6 import sys
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8
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9 def parse_args(args=None):
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10 Description = "Convert iVar variants tsv file to vcf format."
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11 Epilog = """Example usage: python ivar_variants_to_vcf.py <FILE_IN> <FILE_OUT>"""
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13 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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14 parser.add_argument("FILE_IN", help="Input tsv file.")
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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15 parser.add_argument("FILE_OUT", help="Full path to output vcf file.")
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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16 parser.add_argument(
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17 "-po",
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18 "--pass_only",
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19 dest="PASS_ONLY",
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20 help="Only output variants that PASS all filters.",
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21 action="store_true",
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22 )
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23
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24 return parser.parse_args(args)
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25
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26
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27 def make_dir(path):
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28 if not len(path) == 0:
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29 try:
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30 os.makedirs(path)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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31 except OSError as exception:
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32 if exception.errno != errno.EEXIST:
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33 raise
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34
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35
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36 def info_line(info_keys, kv):
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37 info_strings = []
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38 for key in info_keys:
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39 if key not in kv:
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40 raise KeyError(
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41 'Expected key {} missing from INFO field key value pairs'
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42 .format(key)
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43 )
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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44 if kv[key] is False:
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45 # a FLAG element, which should not be set
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46 continue
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47 if kv[key] is True:
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48 # a FLAG element => write the key only
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49 info_strings.append(key)
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50 else:
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51 info_strings.append('{}={}'.format(key, kv[key]))
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52 return ';'.join(info_strings)
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53
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54
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55 def ivar_variants_to_vcf(FileIn, FileOut, passOnly=False):
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56 filename = os.path.splitext(FileIn)[0]
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57 header = (
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58 "##fileformat=VCFv4.2\n"
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59 "##source=iVar\n"
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60 '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n'
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61 '##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
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62 '##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
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63 '##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
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64 '##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
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65 '##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
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66 '##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">\n'
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67 '##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">\n'
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68 '##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n'
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
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69 '##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">'
6
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70 '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
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71 '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
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72 )
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73 info_keys = [
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74 re.match(r'##INFO=<ID=([^,]+),', line).group(1)
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75 for line in header.splitlines()
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76 if line.startswith('##INFO=')
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77 ]
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78 header += (
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79 "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
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80 )
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81
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82 vars_seen = set()
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83 varCountDict = {"SNP": 0, "INS": 0, "DEL": 0}
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84 OutDir = os.path.dirname(FileOut)
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85 make_dir(OutDir)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
86 with open(FileIn) as f, open(FileOut, "w") as fout:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
87 fout.write(header)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
88 for line in f:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
89 if line.startswith("REGION"):
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
90 continue
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
91
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
92 # fields:
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
93 # 0 REGION
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
94 # 1 POS
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
95 # 2 REF
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
96 # 3 ALT
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
97 # 4 REF_DP
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
98 # 5 REF_RV
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
99 # 6 REF_QUAL
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
100 # 7 ALT_DP
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
101 # 8 ALT_RV
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
102 # 9 ALT_QUAL
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
103 # 10 ALT_FREQ
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
104 # 11 TOTAL_DP
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
105 # 12 PVAL
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
106 # 13 PASS
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
107 # 14 GFF_FEATURE
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
108 # 15 REF_CODON
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
109 # 16 REF_AA
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
110 # 17 ALT_CODON
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
111 # 18 ALT_AA
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
112 # 19 POS_AA
6
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
113 line = line.split("\t")
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
114 CHROM = line[0]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
115 POS = line[1]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
116 ID = "."
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
117 REF = line[2]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
118 ALT = line[3]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
119 if ALT[0] == "+":
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
120 ALT = REF + ALT[1:]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
121 var_type = "INS"
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
122 elif ALT[0] == "-":
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
123 REF += ALT[1:]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
124 ALT = line[2]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
125 var_type = "DEL"
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
126 else:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
127 var_type = "SNP"
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
128 QUAL = "."
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
129 pass_test = line[13]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
130 if pass_test == "TRUE":
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
131 FILTER = "PASS"
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
132 else:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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133 FILTER = "FAIL"
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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parents:
diff changeset
134
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
135 if (passOnly and FILTER != "PASS"):
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
136 continue
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
137 var = (CHROM, POS, REF, ALT)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
138 if var in vars_seen:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
139 continue
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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parents:
diff changeset
140
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
141 ref_dp = int(line[4])
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
142 ref_dp_rev = int(line[5])
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
143 ref_dp_fwd = ref_dp - ref_dp_rev
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
144
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
145 alt_dp = int(line[7])
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
146 alt_dp_rev = int(line[8])
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
147 alt_dp_fwd = alt_dp - alt_dp_rev
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
148
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
149 dp4 = f'{ref_dp_fwd},{ref_dp_rev},{alt_dp_fwd},{alt_dp_rev}'
6
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
150 info_elements = {
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
151 'DP': line[11],
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
152 'REF_DP': ref_dp,
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
153 'REF_RV': ref_dp_rev,
6
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
154 'REF_QUAL': line[6],
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
155 'ALT_DP': alt_dp,
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
156 'ALT_RV': alt_dp_rev,
6
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
157 'ALT_QUAL': line[9],
16
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
158 'AF': line[10],
17f911830a8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 6
diff changeset
159 'DP4': dp4
6
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
160 }
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
161 if var_type in ['INS', 'DEL']:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
162 # add INDEL FLAG
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
163 info_elements['INDEL'] = True
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
164 else:
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
165 info_elements['INDEL'] = False
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
166 INFO = info_line(info_keys, info_elements)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
167
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
168 vars_seen.add(var)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
169 varCountDict[var_type] += 1
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
170 fout.write(
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
171 '\t'.join(
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
172 [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
173 ) + '\n'
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
174 )
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
175
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
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176 # Print variant counts to pass to MultiQC
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177 varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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178 print("\t".join(["sample"] + [x[0] for x in varCountList]))
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179 print("\t".join([filename] + [x[1] for x in varCountList]))
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180
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181
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182 def main(args=None):
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183 args = parse_args(args)
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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184 ivar_variants_to_vcf(
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185 args.FILE_IN, args.FILE_OUT, args.PASS_ONLY
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186 )
3bc2ef3d4a17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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187
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188
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189 if __name__ == "__main__":
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190 sys.exit(main())