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mendelian_vote_summary
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mendelian_vote_summary/codescripts/count_mendelian.py

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  1. import pandas as pd

  2. import sys, argparse, os

  3. 

  4. men = pd.read_table(sys.argv[1],header=None,low_memory=False)

  5. vote = pd.read_table(sys.argv[2],low_memory=False)

  6. men[1]=men[1].astype(str)

  7. merged_df = pd.merge(vote, men,  how='inner', left_on=['CHROM','POS'], right_on = [0,1])

  8. lcl5_dat = merged_df[(merged_df[5]!='./.') & (merged_df[5]!='0/0')]

  9. sub = lcl5_dat[['CHROM','POS','REF','ALT',4,5,6,7,8,'LCL5_consensus_calls', 'LCL5_detect_number','LCL5_same_diff',11]]

  10. sub['mendelian_state'] = 'MIE'

  11. sub.loc[sub[11]=='1:1:1','mendelian_state'] = 'MC'

  12. sub.columns=['CHROM','POS','REF','ALT','variant_type','LCL5','LCL6','LCL7','LCL8','LCL5_consensus_calls','LCL5_detect_number','LCL5_same_diff','mendelian_detail','mendelian_state']

  13. sub.to_csv(sys.argv[3],sep="\t",index=0)