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- from __future__ import division
- import sys, argparse, os
- import pandas as pd
- from collections import Counter
-
- # input arguments
- parser = argparse.ArgumentParser(description="this script is to merge mendelian and vcfinfo, and extract high_confidence_calls")
- parser.add_argument('-vcf', '--vcf', type=str, help='merged multiple sample vcf', required=True)
-
-
- args = parser.parse_args()
- vcf = args.vcf
-
- lcl5_outfile = open('LCL5_all_variants.txt','w')
- filtered_outfile = open('LCL5_filtered_variants.txt','w')
-
- vcf_dat = pd.read_table(vcf)
-
-
- for row in vcf_dat.itertuples():
- lcl5_list = [row.Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518,row.Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530,row.Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530, \
- row.Quartet_DNA_BGI_T7_WGE_LCL5_1_20191105,row.Quartet_DNA_BGI_T7_WGE_LCL5_2_20191105,row.Quartet_DNA_BGI_T7_WGE_LCL5_3_20191105, \
- row.Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108,row.Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108,row.Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108, \
- row.Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111,row.Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111,row.Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111, \
- row.Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930,row.Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930,row.Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930, \
- row.Quartet_DNA_ILM_Nova_WUX_LCL5_1_20190917,row.Quartet_DNA_ILM_Nova_WUX_LCL5_2_20190917,row.Quartet_DNA_ILM_Nova_WUX_LCL5_3_20190917, \
- row.Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403,row.Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403,row.Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403, \
- row.Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329,row.Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329,row.Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329, \
- row.Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216,row.Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216,row.Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216]
- lcl5_vcf_gt = [x.split(':')[0] for x in lcl5_list]
- lcl5_gt=[item.replace('./.', '0/0') for item in lcl5_vcf_gt]
- gt_dict = Counter(lcl5_gt)
- highest_gt = gt_dict.most_common(1)
- candidate_gt = highest_gt[0][0]
- freq_gt = highest_gt[0][1]
- output = row._1 + '\t' + str(row.POS) + '\t' + '\t'.join(lcl5_gt) + '\n'
- if (candidate_gt == '0/0') and (freq_gt == 27):
- filtered_outfile.write(output)
- else:
- lcl5_outfile.write(output)
-
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