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updated for formatting quantitative trait
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@pancong419
pancong419 committed Apr 21, 2022
1 parent 1d128ef commit a3676a8
Showing 1 changed file with 32 additions and 6 deletions.
38 changes: 32 additions & 6 deletions GEM2CHARGEGLI_python3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

###################################
### Copyright (C) 2022 Cong Pan ###
### version 0.1, March 4, 2022 ###
### version 0.1, March 4, 2022 ###
###################################

# NOTE: this script is used to convert GEM (v1.4.1 or later) output to the meta-analysis-ready format for Phase2 CHARGE Gene-Lifestyle Interactions projects
Expand Down Expand Up @@ -103,6 +103,12 @@
columns1 = {}
for i in range(len(fields1)):
columns1[fields1[i]] = i
if not "AF_" + Ename + "_0" in columns1 or not "AF_" + Ename + "_1" in columns1 or not "N_" + Ename + "_1" in columns1:
quantE = True
print("quantE is True")
else:
quantE = False
print("quantE is False")
if infile2.endswith(".gz"):
infile2_handle = gzip.open(infile2, "rt", encoding='utf-8')
else:
Expand All @@ -113,7 +119,11 @@
columns2 = {}
for i in range(len(fields2)):
columns2[fields2[i]] = i
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
#outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
if quantE:
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tN\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
else:
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
line_ct = 1
while line1 and line2:
line1 = infile1_handle.readline()
Expand Down Expand Up @@ -183,8 +193,11 @@
else:
p_snp_m1_mb = "{:.6}".format(stats.chi2.sf((float(fields1[columns1["Beta_G"]])/float(fields1[columns1["SE_Beta_G"]]))**2, 1))
p_snp_m1_robust = "{:.6}".format(stats.chi2.sf((float(fields1[columns1["Beta_G"]])/float(fields1[columns1["robust_SE_Beta_G"]]))**2, 1))
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")

#outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
if quantE:
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
else:
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
infile1_handle.close()
infile2_handle.close()

Expand Down Expand Up @@ -253,7 +266,16 @@
for i in range(len(fields2)):
columns2[fields2[i]] = i
if chr == 1:
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
#outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
if not "AF_" + Ename + "_0" in columns1 or not "AF_" + Ename + "_1" in columns1 or not "N_" + Ename + "_1" in columns1:
quantE = True
else:
quantE = False
if quantE:
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tN\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")
else:
outfile_handle.write(b"SNPID\tCHR\tPOS\tINFO\tIMPUTED\tEFFECT_ALLELE\tNON_EFFECT_ALLELE\tEAF_ALL\tEAF_E0\tEAF_E1\tN\tN_EXP\tBETA_SNP_M2\tSE_SNP_M2\tP_SNP_M2\tBETA_SNP_M1\tSE_SNP_M1_MB\tP_SNP_M1_MB\tSE_SNP_M1_ROBUST\tP_SNP_M1_ROBUST\tBETA_INT\tSE_INT_MB\tP_INT_MB\tSE_INT_ROBUST\tP_INT_ROBUST\tP_JOINT_MB\tCOV_SNP_INT_MB\tP_JOINT_ROBUST\tCOV_SNP_INT_ROBUST\n")

line_ct = 1
while line1 and line2:
line1 = infile1_handle.readline()
Expand Down Expand Up @@ -322,7 +344,11 @@
else:
p_snp_m1_mb = "{:.6}".format(stats.chi2.sf((float(fields1[columns1["Beta_G"]])/float(fields1[columns1["SE_Beta_G"]]))**2, 1))
p_snp_m1_robust = "{:.6}".format(stats.chi2.sf((float(fields1[columns1["Beta_G"]])/float(fields1[columns1["robust_SE_Beta_G"]]))**2, 1))
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
#outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
if quantE:
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
else:
outfile_handle.write(str.encode(fields1[columns1["SNPID"]]) + b"\t" + str.encode(fields1[columns1["CHR"]]) + b"\t" + str.encode(fields1[columns1["POS"]]) + b"\t" + str.encode(info[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(imputed[fields1[columns1["SNPID"]]]) + b"\t" + str.encode(fields1[columns1["Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["Non_Effect_Allele"]]) + b"\t" + str.encode(fields1[columns1["AF"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_0"]]) + b"\t" + str.encode(fields1[columns1["AF_" + Ename + "_1"]]) + b"\t" + str.encode(fields1[columns1["N_Samples"]]) + b"\t" + str.encode(fields1[columns1["N_" + Ename + "_1"]]) + b"\t" + str.encode(fields2[columns2["Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["SE_Beta_Marginal"]]) + b"\t" + str.encode(fields2[columns2["P_Value_Marginal"]]) + b"\t" + str.encode(fields1[columns1["Beta_G"]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_mb) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G"]]) + b"\t" + str.encode(p_snp_m1_robust) + b"\t" + str.encode(fields1[columns1["Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["robust_SE_Beta_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Interaction"]]) + b"\t" + str.encode(fields1[columns1["P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["Cov_Beta_G_G-" + Ename]]) + b"\t" + str.encode(fields1[columns1["robust_P_Value_Joint"]]) + b"\t" + str.encode(fields1[columns1["robust_Cov_Beta_G_G-" + Ename]]) + b"\n")
infile1_handle.close()
infile2_handle.close()

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