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mixer_bivar.sh
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mixer_bivar.sh
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phe=0218
for i in $(seq 20 20);do
cmd="python3.8 mixer/mixer-master/precimed/mixer.py fit2 --trait1-file test/cFDR/traitfolder/"$phe".csv_z.csv.gz --trait2-file test/cFDR/traitfolder/MDD2013_noMHC.csv.gz --trait1-params-file test/mixer/result/"$phe".csv_z.csv.gz.fit.rep"$i".json --trait2-params-file test/mixer/result/MDD2013_noMHC.csv.gz.fit.rep"$i".json --out test/mixer/bivar_res/MDD_vs_"$phe".fit.rep"$i" --extract mixer/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep"$i".snps --bim-file mixer/1000G_EUR_Phase3_plink/[email protected] --ld-file mixer/1000G_EUR_Phase3_plink/[email protected] --lib mixer/mixer-master/src/build/lib/libbgmg.so"
echo $cmd > "test/mixer/script/MDD_vs_"$phe"_fit2_"$i".sh"
qsub -q cluster5 -e "test/mixer/script/MDD_vs_"$phe"_fit2_"$i".err" -o "test/mixer/script/MDD_vs_"$phe"_fit2_"$i".out" "test/mixer/script/MDD_vs_"$phe"_fit2_"$i".sh"
done
for i in $(seq 1 20);do
cmd="anaconda/anaconda3/envs/python3.8.8/bin/python3.8 mixer/mixer-master/precimed/mixer.py test2 --trait1-file test/cFDR/traitfolder/"$phe".csv_z.csv.gz --trait2-file test/cFDR/traitfolder/MDD2013_noMHC.csv.gz --load-params-file test/mixer/bivar_res/MDD_vs_"$phe".fit.rep"$i".json --out test/mixer/bivar_res/MDD_vs_"$phe".test2.rep"$i" --bim-file mixer/1000G_EUR_Phase3_plink/[email protected] --ld-file mixer/1000G_EUR_Phase3_plink/[email protected] --lib mixer/mixer-master/src/build/lib/libbgmg.so"
echo $cmd > "test/mixer/script/MDD_vs_"$phe"_test2_"$i".sh"
qsub -q cluster5 -e "test/mixer/script/MDD_vs_"$phe"_test2_"$i".err" -o "test/mixer/script/MDD_vs_"$phe"_test2_"$i".out" "test/mixer/script/MDD_vs_"$phe"_test2_"$i".sh"
done
###-----------------------results
anaconda/anaconda3/envs/python3.8.8/bin/python3.8 mixer/mixer-master/precimed/mixer_figures.py \
combine --json "test/mixer/bivar_res/MDD_vs_"$phe"[email protected]" --out "test/mixer/bivar_res/MDD_vs_"$phe".fit"
anaconda/anaconda3/envs/python3.8.8/bin/python3.8 mixer/mixer-master/precimed/mixer_figures.py \
combine --json test/mixer/bivar_res/MDD_vs_"$phe"[email protected] --out test/mixer/bivar_res/MDD_vs_"$phe".test2
anaconda/anaconda3/envs/python3.8.8/bin/python3.8 mixer/mixer-master/precimed/mixer_figures.py \
two --json-fit test/mixer/bivar_res/MDD_vs_"$phe".fit.json --json-test test/mixer/bivar_res/MDD_vs_"$phe".test2.json \
--out test/mixer/bivar_res/MDD_vs_"$phe"_bivarres --statistic mean std