-
Notifications
You must be signed in to change notification settings - Fork 0
/
run_folds_pt2_and_pt3.sh
70 lines (64 loc) · 4.35 KB
/
run_folds_pt2_and_pt3.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
source constants_.sh
source parse_args.sh "$@"
# discoveries="D2_sysp_evangelou_2018" # "D2_sysp_evangelou_2018,D2_dias_evangelou_2018,D2_asth_zhu_2019,D2_chol_willer_2013,D2_ldlp_willer_2013,D2_t2di_mahajan_2018,D2_gerx_an_2019,D2_madd_howard_2019" # "D2_sysp_evangelou_2018,D2_dias_evangelou_2018,D2_asth_zhu_2019,D2_chol_willer_2013,D2_hdlp_willer_2013,D2_ldlp_willer_2013,D2_t2di_mahajan_2018,D2_gerx_an_2019,D2_madd_howard_2019" # "D2_sysp_evangelou_2018" D2_hdlp_willer_2013
# discoveries="UKB_ht_eur,UKB_chol_eur,UKB_hfvr_eur,UKB_hyty_eur,UKB_madd_eur,UKB_osar_eur,UKB_t2d_eur,UKB_utfi_eur,UKB_gerx_eur,UKB_angna_eur,UKB_ast_eur,UKB_ctrt_eur"
discoveries=${discoveries//,/ }
# targets="ukbb_sas,ukbb_afr" # "ukbb_${pop}"
targets=${targets//,/ }
# imps="impX_new" # "impute2_1kg_gbr,impute2_1kg_eur,impute2_1kg_${pop}" # ,impute2_1kg_afr" # ,impute2_1kg_sas "impute2_1kg_ceu2"
imps=${imps//,/ }
method=${method}
base_rep=105
folds=5
complete_missing=true
if [[ -z ${ld} ]]; then ld="eur"; fi
counter=0
min_n_profiles=9
echo "start with discoveries=${discoveries}, targets=${targets}, imps=${imps}"
for discovery in ${discoveries[@]}; do
if [[ -z ${pheno} ]]; then pheno=${gwas_to_pheno[${discovery}]}; fi
if [[ ! -z ${pheno} ]]; then pheno_param="--pheno ${pheno}"; fi
for target in ${targets[@]}; do
for imp in ${imps[@]}; do
for cur_rep in {1..6}; do
for fold in {1..5}; do
res1=$(ls -1 /specific/netapp5/gaga/gaga-pd/prs_data/PRSs//${discovery}_${target}/${imp}/rep_${base_rep}_${cur_rep}/prs.cv.${method}_${pheno}__${fold}_${folds}_validation.*.profile 2>/dev/null| wc -l ) ;
res3=$(ls -1 /specific/netapp5/gaga/gaga-pd/prs_data/PRSs//${discovery}_${target}/${imp}/rep_${base_rep}_${cur_rep}/prs.cv.${method}_${pheno}__${fold}_${folds}_validation.or.percentile.*.tsv 2>/dev/null | wc -l );
stage=3 # -1
if [[ ${res3} -lt ${min_n_profiles} ]]; then
stage=3
fi
if [[ ${res1} -lt ${min_n_profiles} || ${override} == "true" ]]; then
stage=1
fi
echo "Discovery: ${discovery}, Target: ${target}, imp: ${imp}, rep: ${cur_rep}, fold: ${fold}: res validation: stage 1 - ${res1}, stage 3 - ${res3}"
if [[ ${stage} -ne -1 ]]; then
if [[ ${complete_missing} = true ]]; then
bash calc_prs_cv_${method}.sh --discovery ${discovery} --target ${target} --imp ${imp} --cv ${fold}_${folds} --rep ${base_rep}_${cur_rep} --ld=${ld} --stage ${stage} ${pheno_param};
fi
echo "Discovery: ${discovery}, Target: ${target}, imp: ${imp}, rep: ${cur_rep}, fold: ${fold}: res validation: stage 1 - ${res1}, stage 3 - ${res3}"
counter=$((${counter}+1))
fi
done;
res1=$(ls -1 /specific/netapp5/gaga/gaga-pd/prs_data/PRSs//${discovery}_${target}/${imp}/rep_${base_rep}_${cur_rep}/prs.cv.${method}_${pheno}__${fold}_test.*.profile 2>/dev/null | wc -l);
res3=$(ls -1 /specific/netapp5/gaga/gaga-pd/prs_data/PRSs//${discovery}_${target}/${imp}/rep_${base_rep}_${cur_rep}/prs.cv.${method}_${pheno}__${fold}_test.or.percentile.*.tsv 2>/dev/null | wc -l );
# echo "Discovery: ${discovery}, Target: ${target}, imp: ${imp}, rep: ${cur_rep}, fold: ${fold}: res test: stage 1 - ${res1}, stage 3 - ${res3}"
stage=3 # -1
if [[ ${res3} -lt ${min_n_profiles} ]]; then
stage=3
fi
if [[ ${res1} -lt ${min_n_profiles} || ${override} == "true" ]]; then
stage=1
fi
if [[ ${stage} -ne -1 ]]; then
if [[ ${complete_missing} = true ]]; then
bash calc_prs_cv_${method}.sh --discovery ${discovery} --target ${target} --imp ${imp} --cv 5 --rep ${base_rep}_${cur_rep} --ld=${ld} --stage ${stage} ${pheno_param};
fi
echo "Discovery: ${discovery}, Target: ${target}, imp: ${imp}, rep: ${cur_rep}, fold: ${fold}: res test: stage 1 - ${res1}, stage 3 - ${res3}"
counter=$((${counter}+1))
fi
done
done
done
done
echo "counter: ${counter}"