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test-BBr-local.sh
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test-BBr-local.sh
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source activate py36
folder='/media/storage/UkBiobank/Application_236/R4528/'
csvpath=$folder'ukb4528.csv'
htmlpath=$folder'ukb4528.html'
tsvpath='/media/storage/UkBiobank/HESdata/ukb_HES_236.tsv'
outpath='/media/storage/UkBiobank/Cardiac_GWAS/Extended_data/26k/'
outname='excl_atrial_SR'
##
filterconds='/media/storage/codes/BiobankRead-Bash/filters_test.txt'
varsList=$folder'gen_corr_variable.txt'
#'/media/storage/UkBiobank/Application_236/R4528/VeganVars_2.txt'
withdrawn='/media/storage/UkBiobank/Application_18545/withdrawn_18545_oct2018.csv'
#'/media/storage/codes/BiobankRead-Bash/vars.txt'
ICD10codes='/media/storage/UkBiobank/Cardiac_GWAS/Extended_data/26k/excl_atrial_icd10.txt'
SRpath='/media/storage/UkBiobank/Cardiac_GWAS/Extended_data/26k/excl_atrial_SR.txt'
echo "Output destination: " $oupath$outname
#python Scripts/extract_variables.py \
# --csv $csvpath \
# --html $htmlpath \
# --vars $varsList \
# --visit 0 \
# --combine outer \
# --excl $withdrawn \
# --out $outpath$outname
## --remove_outliers True \
## --filter $filterconds \
## --cov_corr True \
#python Scripts/extract_death.py \
# --csv $csvpath \
# --html $htmlpath \
# --codes 'All' \
# --primary True \
# --secondary True \
# --out $outpath$outname
python Scripts/extract_SR.py \
--csv $csvpath \
--html $htmlpath \
--out $oupath$outname \
--disease $SRpath \
--SRcancer False \
--visit 'all'
#
#python Scripts/extract_HES.py \
# --csv $csvpath \
# --html $htmlpath \
# --out $oupath$outname \
# --tsv $tsvpath \
# --codes $ICD10codes \
# --codeType ICD10 \
# --dateType epistart
# --firstvisit False \
# --baseline False
#
source deactivate