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- from __future__ import division
- import sys, argparse, os
- import fileinput
- import re
- import statistics
-
- # input arguments
- parser = argparse.ArgumentParser(description="this script is to intergeate vcf information, variants quality and location")
-
- parser.add_argument('-vcf', '--multi_sample_vcf', type=str, help='The VCF file you want to count the voting number', required=True)
- parser.add_argument('-prefix', '--prefix', type=str, help='Prefix of output file name', required=True)
-
- args = parser.parse_args()
- multi_sample_vcf = args.multi_sample_vcf
- prefix = args.prefix
-
-
- def get_location(info):
- repeat = ''
- if 'ANN' in info:
- strings = info.strip().split(';')
- for element in strings:
- m = re.match('ANN',element)
- if m is not None:
- repeat = element.split('=')[1]
- else:
- repeat = '.'
- return repeat
-
-
- def extract_info_normal(FORMAT,strings):
- GQ = []
- MQ = []
- DP = []
- ALT = []
- format_strings = FORMAT.split(':')
- for element in strings:
- if element == '.':
- pass
- else:
- element_strings = element.split(':')
- formatDict = dict(zip(format_strings, element_strings))
- alt = int(formatDict['ALT'])
- dp = int(formatDict['DP'])
- gq = int(formatDict['GQ'])
- mq = float(formatDict['MQ'])
- GQ.append(gq)
- MQ.append(mq)
- DP.append(dp)
- ALT.append(alt)
- DP_a = sum(DP)
- ALT_a = sum(ALT)
- if DP_a == 0:
- AF_m = 'NA'
- else:
- AF_m = float(ALT_a/DP_a)
- GQ_m = statistics.mean(GQ)
- MQ_m = statistics.mean(MQ)
- return AF_m,GQ_m,MQ_m,DP_a,ALT_a
-
-
- file_name = prefix + '_variant_quality_location.txt'
- outfile = open(file_name,'w')
- outputcolumn = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tQuartet_DNA_BGI_SEQ2000_BGI_1_20180518_LCL5\tQuartet_DNA_BGI_SEQ2000_BGI_2_20180530_LCL5\tQuartet_DNA_BGI_SEQ2000_BGI_3_20180530_LCL5\tQuartet_DNA_BGI_T7_WGE_1_20191105_LCL5\tQuartet_DNA_BGI_T7_WGE_2_20191105_LCL5\tQuartet_DNA_BGI_T7_WGE_3_20191105_LCL5\tQuartet_DNA_ILM_Nova_ARD_1_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_2_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_3_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_4_20190111_LCL5\tQuartet_DNA_ILM_Nova_ARD_5_20190111_LCL5\tQuartet_DNA_ILM_Nova_ARD_6_20190111_LCL5\tQuartet_DNA_ILM_Nova_BRG_1_20180930_LCL5\tQuartet_DNA_ILM_Nova_BRG_2_20180930_LCL5\tQuartet_DNA_ILM_Nova_BRG_3_20180930_LCL5\tQuartet_DNA_ILM_Nova_WUX_1_20190917_LCL5\tQuartet_DNA_ILM_Nova_WUX_2_20190917_LCL5\tQuartet_DNA_ILM_Nova_WUX_3_20190917_LCL5\tQuartet_DNA_ILM_XTen_ARD_1_20170403_LCL5\tQuartet_DNA_ILM_XTen_ARD_2_20170403_LCL5\tQuartet_DNA_ILM_XTen_ARD_3_20170403_LCL5\tQuartet_DNA_ILM_XTen_NVG_1_20170329_LCL5\tQuartet_DNA_ILM_XTen_NVG_2_20170329_LCL5\tQuartet_DNA_ILM_XTen_NVG_3_20170329_LCL5\tQuartet_DNA_ILM_XTen_WUX_1_20170216_LCL5\tQuartet_DNA_ILM_XTen_WUX_2_20170216_LCL5\tQuartet_DNA_ILM_XTen_WUX_3_20170216_LCL5' +'\t'+ 'location' + '\t' + 'AF' + '\t' + 'GQ' + '\t' + 'MQ' + '\t' + 'DP' + '\t' + 'ALT' +'\n'
- outfile.write(outputcolumn)
-
- for line in fileinput.input(multi_sample_vcf):
- m = re.match('^\#',line)
- if m is not None:
- pass
- else:
- line = line.strip()
- strings = line.split('\t')
- repeat = get_location(strings[7])
- AF,GQ,MQ,DP,ALT = extract_info_normal(strings[8],strings[9:])
- outLine = '\t'.join(strings) + '\t' + repeat +'\t' + str(AF) + '\t' + str(GQ) + '\t' + str(MQ) + '\t' + str(DP) + '\t' + str(ALT) + '\n'
- outfile.write(outLine)
-
-
-
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