Mercurial > repos > dfornika > ivar_variants_to_vcf

annotate ivar_variants_to_vcf.py @ 0:c87f6ad32fd8 draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
author dfornika
date Fri, 05 Jun 2020 05:10:05 +0000
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c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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diff changeset
1 #!/usr/bin/env python
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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2 import os
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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3 import sys
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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4 import re
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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5 import errno
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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6 import argparse
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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7
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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8 def parse_args(args=None):
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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9 Description = 'Convert iVar variants tsv file to vcf format.'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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10 Epilog = """Example usage: python ivar_variants_to_vcf.py <FILE_IN> <FILE_OUT>"""
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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11
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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12 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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13 parser.add_argument('FILE_IN', help="Input tsv file.")
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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14 parser.add_argument('FILE_OUT', help="Full path to output vcf file.")
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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15 parser.add_argument('-po', '--pass_only', dest="PASS_ONLY", help="Only output variants that PASS all filters.",action='store_true')
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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16 parser.add_argument('-ma', '--min_allele_freq', type=float, dest="MIN_ALLELE_FREQ", default=0, help="Only output variants where allele frequency greater than this number (default: 0).")
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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17
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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18 return parser.parse_args(args)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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19
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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20 def make_dir(path):
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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21 if not len(path) == 0:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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22 try:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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23 os.makedirs(path)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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24 except OSError as exception:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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25 if exception.errno != errno.EEXIST:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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26 raise
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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27
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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28 def ivar_variants_to_vcf(FileIn,FileOut,passOnly=False,minAF=0):
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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29 filename = os.path.splitext(FileIn)[0]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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30 header = ('##fileformat=VCFv4.2\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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31 '##source=iVar\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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32 '##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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33 '##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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34 '##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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35 '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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36 '##FORMAT=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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37 '##FORMAT=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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38 '##FORMAT=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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39 '##FORMAT=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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40 '##FORMAT=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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41 '##FORMAT=<ID=ALT_QUAL,Number=1,Type=String,Description="Mean quality of alternate base">\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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42 '##FORMAT=<ID=ALT_FREQ,Number=1,Type=String,Description="Frequency of alternate base">\n')
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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43 header += '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'+filename+'\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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44
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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45 varList = []
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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46 varCountDict = {'SNP':0, 'INS':0, 'DEL':0}
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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47 OutDir = os.path.dirname(FileOut)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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48 make_dir(OutDir)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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49 fout = open(FileOut,'w')
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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50 fout.write(header)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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51 with open(FileIn) as f:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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52 for line in f:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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53 if not re.match("REGION",line):
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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54 line = re.split("\t", line)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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55 CHROM=line[0]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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56 POS=line[1]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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57 ID='.'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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58 REF=line[2]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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59 ALT=line[3]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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60 var_type = 'SNP'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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61 if ALT[0] == '+':
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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62 ALT = REF + ALT[1:]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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63 var_type = 'INS'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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64 elif ALT[0] == '-':
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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65 REF += ALT[1:]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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66 ALT = line[2]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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67 var_type = 'DEL'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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68 QUAL='.'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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69 pass_test=line[13]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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70 if pass_test == 'TRUE':
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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71 FILTER='PASS'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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72 else:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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73 FILTER='FAIL'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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74 INFO='DP='+line[11]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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75 FORMAT='GT:REF_DP:REF_RV:REF_QUAL:ALT_DP:ALT_RV:ALT_QUAL:ALT_FREQ'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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76 SAMPLE='1:'+line[4]+':'+line[5]+':'+line[6]+':'+line[7]+':'+line[8]+':'+line[9]+':'+line[10]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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77 oline = CHROM+'\t'+POS+'\t'+ID+'\t'+REF+'\t'+ALT+'\t'+QUAL+'\t'+FILTER+'\t'+INFO+'\t'+FORMAT+'\t'+SAMPLE+'\n'
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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78 writeLine = True
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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79 if passOnly and FILTER != 'PASS':
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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80 writeLine = False
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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81 if float(line[10]) < minAF:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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82 writeLine = False
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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83 if (CHROM,POS,REF,ALT) in varList:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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84 writeLine = False
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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85 else:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
dfornika
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86 varList.append((CHROM,POS,REF,ALT))
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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87 if writeLine:
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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88 varCountDict[var_type] += 1
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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89 fout.write(oline)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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90 fout.close()
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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91
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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92 ## Print variant counts to pass to MultiQC
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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93 varCountList = [(k, str(v)) for k, v in sorted(varCountDict.items())]
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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94 print('\t'.join(['sample'] + [x[0] for x in varCountList]))
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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95 print('\t'.join([filename] + [x[1] for x in varCountList]))
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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96
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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97 def main(args=None):
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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98 args = parse_args(args)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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99 ivar_variants_to_vcf(args.FILE_IN,args.FILE_OUT,args.PASS_ONLY,args.MIN_ALLELE_FREQ)
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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100
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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101
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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102 if __name__ == '__main__':
c87f6ad32fd8 "planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/ivar_variants_to_vcf commit 16332019b4aab6af58c74e631f390dfeef23a3dc"
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103 sys.exit(main())