11_gwaslab_ldsc.bsub

#!/bin/bash
#BSUB -q long
#BSUB -J gwaslab_ldsc[1-15]
#BSUB -n 16 
#BSUB -R "span[ptile=8]"
#BSUB -R "rusage[mem=16GB]"
#BSUB -o /your/out/dir/gwaslab_%J_%I.out
#BSUB -e /your/err/dir/gwaslab_%J_%I.out

#This script creates gwaslab_ldsc output
#modules
module load anaconda3/2021.05

# activate env
source ~/.bashrc
conda activate /.conda/envs/gwaslab


# Here put your file path
path0=/your/dir/for/sumstats
path1=${path0}Cell_B
path2=${path0}Cell_P
path3=${path0}CLL
path4=${path0}DLBCL
path5=${path0}Drug_G1
path6=${path0}FL
path7=${path0}HL
path8=${path0}LM
path9=${path0}LPL_WM
path10=${path0}MGUS
path11=${path0}MM_MGUS
path12=${path0}MM
path13=${path0}MZL
path14=${path0}Soma_G1
path15=${path0}Soma_G2

#phenotypes
pheno1=Cell_B
pheno2=Cell_P
pheno3=CLL
pheno4=DLBCL
pheno5=Drug_G1
pheno6=FL
pheno7=HL
pheno8=LM
pheno9=LPL_WM
pheno10=MGUS
pheno11=MM_MGUS
pheno12=MM
pheno13=MZL
pheno14=Soma_G1
pheno15=Soma_G2

# array
combined1=path${LSB_JOBINDEX}
combined2=pheno${LSB_JOBINDEX}



cd ${!combined1}

# run Python code
python3 - "${!combined1}" "${!combined2}" <<EOF
import gwaslab as gl
import sys

combined1 = sys.argv[1]
combined2 = sys.argv[2]

globals()[combined2] = gl.Sumstats(
    f"{combined2}_out_A1FREQ0p001_info0p9.txt.gz",
    snpid="SNP",
    chrom="CHROM",
    pos="GENPOS",
    ea="ALLELE1",
    nea="ALLELE0",
    eaf="A1FREQ",
    beta="BETA",
    se="SE",
    mlog10p="LOG10P",
    chisq="CHISQ",
    info="INFO",
    n="N",
    other=["EXTRA"],
    ncase="N_CASES",
    ncontrol="N_CONTROLS",
    sep=" "
)
globals()[combined2].basic_check()

import numpy as np
import scipy.stats as ss

globals()[combined2].fill_data(to_fill=["P","Z","OR","OR_95L","OR_95U"])


globals()[combined2].assign_rsid( 
                        ref_rsid_tsv = gl.get_path("1kg_dbsnp151_hg19_auto"),
                        ref_rsid_vcf = "/./asset/GCF_000001405.25.gz",
                        chr_dict = gl.get_number_to_NC(build="19"),
                        n_cores = 16)



globals()[combined2].to_format(f"{combined2}_ldsc",fmt="ldsc")


# Additional Python code if needed
EOF