Mercurial > repos > iuc > ivar_removereads

annotate ivar_variants_to_vcf.py @ 14:f57ce5d5c997 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 51d656555f9635bb8988f9eec904ee66657736e1
author iuc
date Wed, 19 Apr 2023 08:31:49 +0000
parents 61507c9d063e
children 69797fa273c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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61507c9d063e "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
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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2 import argparse
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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3 import errno
61507c9d063e "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
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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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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12
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13 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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14 parser.add_argument("FILE_IN", help="Input tsv file.")
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15 parser.add_argument("FILE_OUT", help="Full path to output vcf file.")
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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)
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31 except OSError as exception:
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32 if exception.errno != errno.EEXIST:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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33 raise
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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:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
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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 )
61507c9d063e "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'
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69 '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
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70 '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
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71 )
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72 info_keys = [
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73 re.match(r'##INFO=<ID=([^,]+),', line).group(1)
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74 for line in header.splitlines()
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75 if line.startswith('##INFO=')
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76 ]
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77 header += (
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78 "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
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79 )
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80
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81 vars_seen = set()
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82 varCountDict = {"SNP": 0, "INS": 0, "DEL": 0}
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83 OutDir = os.path.dirname(FileOut)
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84 make_dir(OutDir)
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85 with open(FileIn) as f, open(FileOut, "w") as fout:
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86 fout.write(header)
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87 for line in f:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
88 if line.startswith("REGION"):
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
89 continue
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
90
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
91 line = line.split("\t")
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
92 CHROM = line[0]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
93 POS = line[1]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
94 ID = "."
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
95 REF = line[2]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
96 ALT = line[3]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
97 if ALT[0] == "+":
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
98 ALT = REF + ALT[1:]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
99 var_type = "INS"
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
100 elif ALT[0] == "-":
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
101 REF += ALT[1:]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
102 ALT = line[2]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
103 var_type = "DEL"
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
104 else:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
105 var_type = "SNP"
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
106 QUAL = "."
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
107 pass_test = line[13]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
108 if pass_test == "TRUE":
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
109 FILTER = "PASS"
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
110 else:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
111 FILTER = "FAIL"
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
112
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
113 if (passOnly and FILTER != "PASS"):
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
114 continue
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
115 var = (CHROM, POS, REF, ALT)
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
116 if var in vars_seen:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
117 continue
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
118
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
119 info_elements = {
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
120 'DP': line[11],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
121 'REF_DP': line[4],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
122 'REF_RV': line[5],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
123 'REF_QUAL': line[6],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
124 'ALT_DP': line[7],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
125 'ALT_RV': line[8],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
126 'ALT_QUAL': line[9],
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
127 'AF': line[10]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
128 }
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
129 if var_type in ['INS', 'DEL']:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
130 # add INDEL FLAG
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
131 info_elements['INDEL'] = True
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
132 else:
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
133 info_elements['INDEL'] = False
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
134 INFO = info_line(info_keys, info_elements)
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
135
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
136 vars_seen.add(var)
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
137 varCountDict[var_type] += 1
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
138 fout.write(
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
139 '\t'.join(
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
140 [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
141 ) + '\n'
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
142 )
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
143
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
144 # Print variant counts to pass to MultiQC
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
145 varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
146 print("\t".join(["sample"] + [x[0] for x in varCountList]))
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
147 print("\t".join([filename] + [x[1] for x in varCountList]))
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
148
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
149
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
150 def main(args=None):
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
151 args = parse_args(args)
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
152 ivar_variants_to_vcf(
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
153 args.FILE_IN, args.FILE_OUT, args.PASS_ONLY
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
154 )
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
155
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
156
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
157 if __name__ == "__main__":
61507c9d063e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
diff changeset
158 sys.exit(main())