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fishnet.sh
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#!/bin/bash -ue
######################################
# Master script for FISHNET pipeline #
######################################
usage() {
cat << EOF
Master script for the FISHNET pipeline
Usage: fishnet.sh [options]
Options:
-h, --help
Prints the command usage
Default: false
--test
Runs the test configuration
Default: true
--skip-stage-1
Skips stage 1 of FISHNET
Default: false
--skip-stage-2
Skips stage 2 of FISHNET
Default: false
--thresholding-alternative
Configures stage 2 to run alternative thresholding mechanism
Default: false (runs default thresholding mechanism)
--singularity
Configures containers to run using singularity
Default: false (runs containers using docker)
--nxf-config <path/to/nxf.config>
Specify a custom nextflow config to use
Default: ./conf/fishnet.config using docker, ./conf/fishnet_slurm.config using singularity on SLURM
--FDR-threshold <float>
Specify a custom FDR threshold cutoff
Default: 0.05
--percentile-threshold <float>
Specify a custom percentile threshold cutoff
Default: 0.99
--num-permutations <integer>
Configures the number of permutations
Default: 10
--trait <path/to/input/file.csv>
Path to the input summary statistics file.
File must be a CSV file with colnames "Genes" and "p_vals".
Filename must not include any '_', '-', or '.' characters.
(Refer to ./test/maleWC/maleWC.csv for an example)
--modules <path/to/modules/directory/>
Path to directory containing network modules.
Network module files must be tab-delimited .txt files
(Refer to ./test/ker_based/ for examples)
EOF
}
TEST_MODE=false
SKIP_STAGE_1=false
SKIP_STAGE_2=false
THRESHOLDING_MODE_DEFAULT="default"
THRESHOLDING_MODE_ALTERNATIVE="alternative"
THRESHOLDING_MODE=$THRESHOLDING_MODE_DEFAULT
SINGULARITY=false
CONTAINER_RUNTIME="DOCKER"
NXF_CONFIG_DEFAULT_DOCKER="./conf/fishnet.config"
NXF_CONFIG_DEFAULT_SINGULARITY="./conf/fishnet_slurm.config"
NXF_CONFIG="$NXF_CONFIG_DEFAULT_DOCKER"
nxf_config_provided=false
OUTPUT_DIR=$( readlink -f "./results/" )
DATADIR="${OUTPUT_DIR}/data/"
MODULEDIR="${DATADIR}/modules/"
GENECOLNAME="Genes"
PVALCOLNAME="p_vals"
BONFERRONI_ALPHA=0.05 # for phase 1 nextflow scripts
# parameters
FDR_THRESHOLD=0.05
PERCENTILE_THRESHOLD=0.99
NUM_PERMUTATIONS=10
TRAITPATH="NONE"
# print usage if no args
if [ "$#" -eq 0 ]; then
usage
exit 1
fi
# parse args
while [[ $# -gt 0 ]]; do
case "$1" in
-h|--help)
usage
exit 0
;;
--test)
TEST_MODE=true
shift
;;
--skip-stage-1)
SKIP_STAGE_1=true
shift
;;
--skip-stage-2)
SKIP_STAGE_2=true
shift
;;
--thresholding-alternative)
THRESHOLDING_MODE=$THRESHOLDING_MODE_ALTERNATIVE
shift
;;
--singularity)
SINGULARITY=true
CONTAINER_RUNTIME="SINGULARITY"
shift
;;
--nxf-config)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
NXF_CONFIG="$2"
nxf_config_provided=true
shift 2
else
echo "ERROR: --nxf-config requires a path argument."
exit 1
fi
;;
--FDR-threshold)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
FDR_THRESHOLD="$2"
shift 2
else
echo "ERROR: --FDR-threshold requires a float argument."
exit 1
fi
;;
--percentile-threshold)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
PERCENTILE_THRESHOLD="$2"
shift 2
else
echo "ERROR: --percentile-threshold requires a float argument."
exit 1
fi
;;
--trait)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
TRAITPATH="$2"
shift 2
else
echo "ERROR: --trait requires a string path argument."
exit 1
fi
;;
--modules)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
INPUTMODULEDIR="$2"
shift 2
else
echo "ERROR: --modules requires a string path argument."
exit 1
fi
;;
--num-permutations)
# make sure we have a value and not another flag
if [[ -n "$2" && ! "$2" =~ ^- ]]; then
NUM_PERMUTATIONS="$2"
shift 2
else
echo "ERROR: --num-permutations requires an integer argument."
exit 1
fi
;;
*)
echo "ERROR: Unknown option $1"
usage
exit 1
;;
esac
done
# check if both stage skip flags have been set
if [ "$SKIP_STAGE_1" = true ] && [ "$SKIP_STAGE_2" = true ]; then
echo "Both --skip-stage-1 and --skip-stage-2 provided. Nothing to do. Exiting."
exit 0
fi
# check for singularity
if [ "$SINGULARITY" = true ]; then
# if singularity requested, but user did not specify --nxf_config
if [ "$nxf_config_provided" = false ]; then
NXF_CONFIG="$NXF_CONFIG_DEFAULT_SINGULARITY"
fi
fi
# print configs
echo "Configs:"
echo " - container run-time: $CONTAINER_RUNTIME"
if [ "$CONTAINER_RUNTIME" = "SINGULARITY" ]; then
singularity --version
else
docker --version
fi
echo " - nextflow config: $NXF_CONFIG"
### set test parameters ###
if [ "$TEST_MODE" = true ]; then
TRAITPATH="./test/maleWC/maleWC.csv"
INPUTMODULEDIR="./test/ker_based/"
else
# check for required input parameters
# input trait file
if [ ! -f "$TRAITPATH" ]; then
echo "--trait $TRAITPATH FILE NOT FOUND"
exit 1
fi
# input modules directory
if [ ! -d "$INPUTMODULEDIR" ]; then
echo "--modules $INPUTMODULEDIR DIRECTORY NOT FOUND"
exit 1
fi
fi
# process input pval file #
filebasename=$( basename $TRAITPATH )
TRAIT="${filebasename%.*}"
TRAITRR="${TRAIT}RR"
# copy over input pval file
PVALFILEDIR="${DATADIR}/${TRAIT}"
PVALFILEDIRRR="${DATADIR}/${TRAITRR}"
mkdir -p $PVALFILEDIR $PVALFILEDIRRR
PVALFILEPATH="${PVALFILEDIR}/0-${TRAIT}.csv"
PVALFILEPATHRR="${PVALFILEDIRRR}/${TRAITRR}.csv"
cp $TRAITPATH $PVALFILEPATH
NUMTESTS=$(( $(wc -l < "$PVALFILEPATH") - 1 ))
# copy over input modules files
mkdir -p $MODULEDIR
cp -r $INPUTMODULEDIR $MODULEDIR
MODULE_ALGO=$( basename $INPUTMODULEDIR )
MODULEFILEDIR=${MODULEDIR}/${MODULE_ALGO}
### export parameters ###
export TRAIT
export TRAITRR
export NUM_PERMUTATIONS
export PVALFILEDIR
export PVALFILEPATH
export PVALFILEPATHRR
export MODULE_ALGO
export MODULEFILEDIR
export NUMTESTS
export GENECOLNAME
export PVALCOLNAME
export BONFERRONI_ALPHA
export OUTPUT_DIR
export FDR_THRESHOLD
export PERCENTILE_THRESHOLD
export NXF_CONFIG
### list of containers ###
# contains all python dependencies for fishnet
# TODO: create single container with all python dependencies (include statsmodels)
# TODO: add to biocontainers
export container_python="docker://jungwooseok/dc_rp_genes:1.0"
export container_R="docker://jungwooseok/r-webgestaltr:1.0"
#################
### FUNCTIONS ###
#################
phase1_step1() {
# (1) nextflow original run
echo "# STEP 1.1: executing Nextflow MEA pipeline on original run"
if [ "$SINGULARITY" = true ]; then
JOB_STAGE1_STEP1=$(sbatch ./scripts/phase1/phase1_step1.sh $(pwd))
JOB_STAGE1_STEP1_ID=$(echo "$JOB_STAGE1_STEP1" | awk '{print $4}')
else
./scripts/phase1/phase1_step1.sh $(pwd)
fi
# (4.1) original
summaries_path_original="${OUTPUT_DIR}/masterSummaries/summaries/"
if [ "$SINGULARITY" = true ]; then
JOB_STAGE1_STEP4_ORIGINAL=$(sbatch --dependency=afterok:"$JOB_STAGE1_STEP1_ID" <<EOT
#!/bin/bash
#SBATCH -J phase1_step4_original
#SBATCH -o ./logs/phase1_step4_original_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase1/compile_results.py \
--dirPath $summaries_path_original \
--identifier $TRAIT \
--output $OUTPUT_DIR
EOT
)
JOB_STAGE1_STEP4_ORIGINAL_ID=$(echo "$JOB_STAGE1_STEP4_ORIGINAL" | awk '{print $4}')
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase1/compile_results.py \
--dirPath $summaries_path_original \
--identifier $TRAIT \
--output $OUTPUT_DIR"
fi
}
phase1_step2() {
# (2) generate uniform p-values
echo "# STEP 1.2: generating uniformly distributed p-values"
if [ "$SINGULARITY" = true ]; then
sbatch <<EOT
#!/bin/bash
#SBATCH -J phase1_step2
#SBATCH -o ./logs/phase1_step2_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase1/generate_uniform_pvals.py \
--genes_filepath $PVALFILEPATH
EOT
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase1/generate_uniform_pvals.py \
--genes_filepath $PVALFILEPATH"
fi
}
phase1_step3() {
# (3) nextflow random permutation run
echo "# STEP 1.3: executing Nextflow MEA pipeline on random permutations"
echo "executing Nextflow MEA pipeline on random permutations"
if [ "$SINGULARITY" = true ]; then
JOB_STAGE1_STEP3=$(sbatch ./scripts/phase1/phase1_step3.sh $(pwd))
JOB_STAGE1_STEP3_ID=$(echo "$JOB_STAGE1_STEP3" | awk '{print $4}')
else
./scripts/phase1/phase1_step3.sh $(pwd)
fi
# (4.2)
summaries_path_permutation="${OUTPUT_DIR}/masterSummaries_RP/summaries/"
if [ "$SINGULARITY" = true ]; then
JOB_STAGE1_STEP4_PERMUTATION=$(sbatch --dependency=afterok:"$JOB_STAGE1_STEP3_ID" <<EOT
#!/bin/bash
#SBATCH -J phase1_step4_permutation
#SBATCH -o ./logs/phase1_step4_permutation_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase1/compile_results.py \
--dirPath $summaries_path_permutation \
--identifier ${TRAITRR} \
--output $OUTPUT_DIR
EOT
)
JOB_STAGE1_STEP4_PERMUTATION_ID=$(echo "$JOB_STAGE1_STEP4_PERMUTATION" | awk '{print $4}')
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase1/compile_results.py \
--dirPath $summaries_path_permutation \
--identifier ${TRAITRR} \
--output $OUTPUT_DIR"
fi
}
phase1_step5() {
# (5) organize phase 1 results
echo "# STEP 5: restructuring phase 1 results for input to phase 2"
# TODO: consider defining shell functions in separate file
# function to organize phase 1 nextflow pipeline results
if [ "$SINGULARITY" = true ]; then
JOB_STAGE1_STEP5=$(sbatch --dependency=afterok:"$JOB_STAGE1_STEP4_ORIGINAL_ID","$JOB_STAGE1_STEP4_PERMUTATION_ID" <<EOT
#!/bin/bash
#SBATCH -J phase1_step5
#SBATCH -o ./logs/phase1_step5_%J.out
organize_nextflow_results() {
trait=\$1
results_dir=\$2
traitRR=\$3
# create outer trait directories
trait_dir="\${results_dir}/\${trait}/"
traitRR_dir="\${results_dir}/\${traitRR}/"
mkdir -p \$trait_dir \$traitRR_dir
# move over original results
mv "\${results_dir}/GO_summaries" \${trait_dir}
mv "\${results_dir}/masterSummaries" \${trait_dir}
mv "\${results_dir}/master_summary_\${trait}.csv" \${trait_dir}/master_summary.csv
# 3. move over permutation results
mv "\${results_dir}/GO_summaries_RP" "\${traitRR_dir}/GO_summaries"
mv "\${results_dir}/masterSummaries_RP" "\${traitRR_dir}/masterSummaries"
mv "\${results_dir}/master_summary_\${traitRR}.csv" \${traitRR_dir}/master_summary.csv
}
organize_nextflow_results $TRAIT $OUTPUT_DIR $TRAITRR
EOT
)
JOB_STAGE1_STEP5_ID=$(echo "$JOB_STAGE1_STEP5" | awk '{print $4}')
else
organize_nextflow_results() {
trait=$1
results_dir=$2
traitRR="${TRAITRR}"
# create outer trait directories
trait_dir="${results_dir}/${TRAIT}/"
traitRR_dir="${results_dir}/${TRAITRR}/"
mkdir -p $TRAIT_dir $TRAITRR_dir
# move over original results
mv "${results_dir}/GO_summaries" ${trait_dir}
mv "${results_dir}/masterSummaries" ${trait_dir}
mv "${results_dir}/master_summary_${TRAIT}.csv" ${trait_dir}/master_summary.csv
# 3. move over permutation results
mv "${results_dir}/GO_summaries_RP" "${traitRR_dir}/GO_summaries"
mv "${results_dir}/masterSummaries_RP" "${traitRR_dir}/masterSummaries"
mv "${results_dir}/master_summary_${TRAITRR}.csv" ${traitRR_dir}/master_summary.csv
}
organize_nextflow_results $TRAIT $OUTPUT_DIR
fi
}
phase2_step0() {
# (0) filter the summary file for original/permuted runs
echo "# STEP 2.0: filtering + parsing master_summary.csv files"
( head -n 1 "${OUTPUT_DIR}/${TRAIT}/master_summary.csv"; grep 'True' "${OUTPUT_DIR}/${TRAIT}/master_summary.csv" ) > "${OUTPUT_DIR}/${TRAIT}/master_summary_filtered.csv"
cut -d ',' -f 1-8 "${OUTPUT_DIR}/${TRAIT}/master_summary_filtered.csv" > "${OUTPUT_DIR}/${TRAIT}/master_summary_filtered_parsed.csv"
( head -n 1 "${OUTPUT_DIR}/${TRAITRR}/master_summary.csv"; grep 'True' "${OUTPUT_DIR}/${TRAITRR}/master_summary.csv" ) > "${OUTPUT_DIR}/${TRAITRR}/master_summary_filtered.csv"
cut -d ',' -f 1-8 "${OUTPUT_DIR}/${TRAITRR}/master_summary_filtered.csv" > "${OUTPUT_DIR}/${TRAITRR}/master_summary_filtered_parsed.csv"
}
phase2_step1_default() {
## (1) generate statistics for original run
echo "# STEP 2.1: generating statistics for original run"
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP1_DEFAULT=$(sbatch <<EOT
#!/bin/bash
#SBATCH -J phase2_step1_default
#SBATCH --array=1-$num_networks
#SBATCH -o ./logs/phase2_step1_default_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_generate_or_statistics.py \
--gene_set_path $PVALFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/master_summary_filtered_parsed.csv \
--trait $TRAIT \
--module_path ${MODULEFILEDIR}/\${network}.txt \
--go_path ${OUTPUT_DIR}/${TRAIT}/GO_summaries/${TRAIT}/ \
--study $TRAIT \
--output_path ${OUTPUT_DIR}/${TRAIT}/results/raw/ \
--network \$network
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP1_DEFAULT_ID=$(echo "$JOB_STAGE2_STEP1_DEFAULT" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_generate_or_statistics.py \
--gene_set_path $PVALFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/master_summary_filtered_parsed.csv \
--trait $TRAIT \
--module_path ${MODULEFILEDIR}/${network}.txt \
--go_path ${OUTPUT_DIR}/${TRAIT}/GO_summaries/${TRAIT}/ \
--study $TRAIT \
--output_path ${OUTPUT_DIR}/${TRAIT}/results/raw/ \
--network $network"
done
fi
}
create_tmp_threshold_network_pairs_default() {
# 1. take 25% of number of genes form original p-values input file
#pct_25=$( bc <<< "scale=2; 0.25 * $NUMTESTS" )
#rounded_25=$( printf "%.0f" "$pct_25" )
rounded_25=$(( (25 * NUMTESTS + 50) / 100 ))
# 2. range 10..{1} take nearest multiple of 10
max_threshold=$(( rounded_25 - (rounded_25 % 10) ))
thresholds=()
for (( i=10; i<=max_threshold; i+=10 )); do
thresholds+=( "$i" )
done
modules=( $( ls ./test/ker_based/*.txt ) )
for f in "${modules[@]}"; do
base="$(basename "$f" .txt )"
for t in "${thresholds[@]}"; do
echo -e "${t}\t${base}"
done
done
}
phase2_step2_default() {
# (2.2) generate statistics for permutation run
echo "# STEP 2.2: generating statistics for permutation runs"
genes_rpscores_filedir="./results/RPscores/${TRAITRR}/"
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
create_tmp_threshold_network_pairs_default > $tmpfile
if [ "$SINGULARITY" = true ]; then
num_pairs=$( wc -l < $tmpfile )
JOB_STAGE2_STEP2_DEFAULT=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP1_DEFAULT_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step2_default
#SBATCH --array=1-$num_pairs
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step2_default_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile | cut -f 2 )
threshold=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile | cut -f 1 )
echo \$network
echo \$threshold
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_generate_rp_statistics.py \
--gene_set_path $genes_rpscores_filedir \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/master_summary_filtered_parsed.csv \
--trait ${TRAITRR} \
--module_path ${MODULEFILEDIR}/\${network}.txt \
--go_path ${OUTPUT_DIR}/${TRAITRR}/GO_summaries/${TRAITRR}/ \
--output_path ${OUTPUT_DIR}/${TRAITRR}/results/raw/ \
--network \$network \
--threshold \$threshold \
--num_permutations ${NUM_PERMUTATIONS}
EOT
)
JOB_STAGE2_STEP2_DEFAULT_ID=$(echo "$JOB_STAGE2_STEP2_DEFAULT" | awk '{print $4}')
else
while IFS=$'\t' read -r threshold network; do
echo "Threshold $threshold, Network: $network"
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_generate_rp_statistics.py \
--gene_set_path $genes_rpscores_filedir \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/master_summary_filtered_parsed.csv \
--trait ${TRAITRR} \
--module_path ${MODULEFILEDIR}/${network}.txt \
--go_path ${OUTPUT_DIR}/${TRAITRR}/GO_summaries/${TRAITRR}/ \
--output_path ${OUTPUT_DIR}/${TRAITRR}/results/raw/ \
--network $network \
--threshold $threshold \
--num_permutations $NUM_PERMUTATIONS"
done < $tmpfile
fi
#rm -rf $tmpfile
}
phase2_step3_default() {
# (3) summarize statistics
echo "# STEP 2.3: summarizing statistics"
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP3_DEFAULT=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP2_DEFAULT_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step3_default
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step3_default_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_summary_statistics_rp.py \
--trait $TRAIT \
--input_path $OUTPUT_DIR \
--or_id $TRAIT \
--rr_id $TRAITRR \
--input_file_rr_id $TRAITRR \
--network \$network \
--output_path ${OUTPUT_DIR}/${TRAIT}/summary/
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP3_DEFAULT_ID=$(echo "$JOB_STAGE2_STEP3_DEFAULT" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_summary_statistics_rp.py \
--trait $TRAIT \
--input_path $OUTPUT_DIR \
--or_id $TRAIT \
--rr_id ${TRAITRR} \
--input_file_rr_id ${TRAITRR} \
--network $network \
--output_path ${OUTPUT_DIR}/${TRAIT}/summary/"
done
fi
}
phase2_step4_default() {
# (4) identify MEA passing genes
echo "# STEP 2.4: identify MEA-passing genes"
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP4_DEFAULT=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP3_DEFAULT_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step4_default
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step4_default_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_identify_mea_passing_genes.py \
--trait $TRAIT \
--geneset_input $PVALFILEDIR\
--FDR_threshold $FDR_THRESHOLD \
--percentile_threshold $PERCENTILE_THRESHOLD \
--network \$network \
--input_path ${OUTPUT_DIR}/${TRAIT}
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP4_DEFAULT_ID=$(echo "$JOB_STAGE2_STEP4_DEFAULT" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_identify_mea_passing_genes.py \
--trait $TRAIT \
--geneset_input $PVALFILEDIR\
--FDR_threshold $FDR_THRESHOLD \
--percentile_threshold $PERCENTILE_THRESHOLD \
--network $network \
--input_path ${OUTPUT_DIR}/${TRAIT}"
done
fi
}
phase2_step1_alternate() {
# (1) generate background gene sets for GO analysis
echo "# STEP 1: generating background gene sets for GO analysis"
if [ "$SINGULARITY" = true ]; then
JOB_STAGE2_STEP1_ALTERNATE=$(sbatch <<EOT
#!/bin/bash
#SBATCH -J phase2_step1_alternate
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step1_alternate_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_fishnet_background_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--output_filepath ${OUTPUT_DIR}/${TRAIT}/
# (1.1) copy background genes to permutation directory
cp -r ${OUTPUT_DIR}/${TRAIT}/background_genes/ ${OUTPUT_DIR}/${TRAITRR}/
EOT
)
JOB_STAGE2_STEP1_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP1_ALTERNATE" | awk '{print $4}')
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_fishnet_background_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--output_filepath ${OUTPUT_DIR}/${TRAIT}/"
# (1.1) copy background genes to permutation directory
cp -r ${OUTPUT_DIR}/${TRAIT}/background_genes/ ${OUTPUT_DIR}/${TRAITRR}/
fi
}
phase2_step2_original_alternate() {
# (2) Extract and save module genes as individual files for modules that satisfy Bonferroni 0.25
echo "# STEP 2.1: extract and save modules that satisfy Bonferroni threshold (original run)"
# (2.1) original run
if [ "$SINGULARITY" = true ]; then
JOB_STAGE2_STEP2_ORIGINAL_ALTERNATE=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP1_ALTERNATE_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step2_original_alternate
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step2_original_alternate_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_fishnet_module_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/ \
--study $TRAIT
EOT
)
JOB_STAGE2_STEP2_ORIGINAL_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP2_ORIGINAL_ALTERNATE" | awk '{print $4}')
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_fishnet_module_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/ \
--study $TRAIT"
fi
}
phase2_step2_permutation_alternate() {
# (2) Extract and save module genes as individual files for modules that satisfy Bonferroni 0.25
echo "# STEP 2.2: extract and save modules that satisfy Bonferroni threshold (permutation run)"
# (2.2) permutation run
if [ "$SINGULARITY" = true ]; then
JOB_STAGE2_STEP2_PERMUTATION_ALTERNATE=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP1_ALTERNATE_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step2_permutation_alternate
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step2_permutation_alternate_%J.out
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_fishnet_module_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/ \
--study $TRAITRR
EOT
)
JOB_STAGE2_STEP2_PERMUTATION_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP2_PERMUTATION_ALTERNATE" | awk '{print $4}')
else
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_fishnet_module_genes.py \
--genes_filepath $PVALFILEPATHRR \
--module_filepath $MODULEFILEDIR \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/ \
--study $TRAITRR"
fi
}
phase2_step3_original_alternate() {
# (3) Run GO analysis
echo "# STEP 3.1: running GO analysis (original run)"
# (3.1) original run
set +e
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP3_ORIGINAL_ALTERNATE=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP2_ORIGINAL_ALTERNATE_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step3_original_alternate
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step3_original_alternate_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_R \
Rscript ./scripts/phase2/dc_ORA_cmd.R \
--sigModuleDir ${OUTPUT_DIR}/${TRAIT}/enriched_modules/${TRAIT}-\${network}/ \
--backGroundGenesFile ${OUTPUT_DIR}/${TRAIT}/background_genes/${MODULE_ALGO}-\${network}.txt \
--summaryRoot ${OUTPUT_DIR}/${TRAIT}/GO_summaries_alternate/ \
--reportRoot ${OUTPUT_DIR}/${TRAIT}/report_sumamries_alternate/
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP3_ORIGINAL_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP3_ORIGINAL_ALTERNATE" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_R /bin/bash -c \
"Rscript ./scripts/phase2/dc_ORA_cmd.R \
--sigModuleDir ${OUTPUT_DIR}/${TRAIT}/enriched_modules/${TRAIT}-${network}/ \
--backGroundGenesFile ${OUTPUT_DIR}/${TRAIT}/background_genes/${MODULE_ALGO}-${network}.txt \
--summaryRoot ${OUTPUT_DIR}/${TRAIT}/GO_summaries_alternate/ \
--reportRoot ${OUTPUT_DIR}/${TRAIT}/report_sumamries_alternate/"
done
fi
set -e
}
phase2_step3_permutation_alternate() {
# (3) Run GO analysis
echo "# STEP 3.1: running GO analysis (permutation run)"
# (3.2) permutation run
set +e
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP3_PERMUTATION_ALTERNATE=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP2_PERMUTATION_ALTERNATE_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step3_permutation_alternate
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step3_permutation_alternate_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_R \
Rscript ./scripts/phase2/dc_ORA_cmd.R \
--sigModuleDir ${OUTPUT_DIR}/${TRAITRR}/enriched_modules/${TRAITRR}-\${network}/ \
--backGroundGenesFile ${OUTPUT_DIR}/${TRAITRR}/background_genes/${MODULE_ALGO}-\${network}.txt \
--summaryRoot ${OUTPUT_DIR}/${TRAITRR}/GO_summaries_alternate/ \
--reportRoot ${OUTPUT_DIR}/${TRAITRR}/report_sumamries_alternate/
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP3_PERMUTATION_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP3_PERMUTATION_ALTERNATE" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_R /bin/bash -c \
"Rscript ./scripts/phase2/dc_ORA_cmd.R \
--sigModuleDir ${OUTPUT_DIR}/${TRAITRR}/enriched_modules/${TRAITRR}-${network}/ \
--backGroundGenesFile ${OUTPUT_DIR}/${TRAITRR}/background_genes/${MODULE_ALGO}-${network}.txt \
--summaryRoot ${OUTPUT_DIR}/${TRAITRR}/GO_summaries_alternate/ \
--reportRoot ${OUTPUT_DIR}/${TRAITRR}/report_sumamries_alternate/"
done
fi
set -e
}
phase2_step4_alternate() {
# (4) Generate statistics for original gene-level p-values
echo "# STEP 4: generate statistics for original gene-level p-values"
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP4_ALTERNATE=$(sbatch --dependency=afterany:"$JOB_STAGE2_STEP3_ORIGINAL_ALTERNATE_ID" <<EOT
#!/bin/bash
#SBATCH -J phase2_step4_alternate
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step4_alternate_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
echo "Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_generate_or_statistics_alternate.py \
--gene_set_path ${PVALFILEDIR} \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/master_summary_alternate.csv \
--trait $TRAIT \
--module_path ${OUTPUT_DIR}/${TRAIT}/enriched_modules/${TRAIT}-\${network}/ \
--go_path ${OUTPUT_DIR}/${TRAIT}/GO_summaries_alternate/ \
--study $TRAIT \
--output_path ${OUTPUT_DIR}/${TRAIT}/results/raw_alternate/ \
--network \$network
EOT
)
#rm $tmpfile
JOB_STAGE2_STEP4_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP4_ALTERNATE" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_generate_or_statistics_alternate.py \
--gene_set_path ${PVALFILEDIR} \
--master_summary_path ${OUTPUT_DIR}/${TRAIT}/master_summary_alternate.csv \
--trait $TRAIT \
--module_path ${OUTPUT_DIR}/${TRAIT}/enriched_modules/${TRAIT}-${network}/ \
--go_path ${OUTPUT_DIR}/${TRAIT}/GO_summaries_alternate/ \
--study $TRAIT \
--output_path ${OUTPUT_DIR}/${TRAIT}/results/raw_alternate/ \
--network $network"
done
fi
}
create_tmp_threshold_network_pairs_alternate() {
thresholds=(0.00005 0.0001 0.005 0.01 0.05 0.1 0.15 0.2 0.25)
modules=( $( ls ./test/ker_based/*.txt ) )
for f in "${modules[@]}"; do
base="$(basename "$f" .txt )"
for t in "${thresholds[@]}"; do
echo -e "${t}\t${base}"
done
done
}
phase2_step5_alternate() {
# (5) Generate statistics for random permutation runs
echo "# STEP 5: generate statistics for random permutations"
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
create_tmp_threshold_network_pairs_alternate > $tmpfile
if [ "$SINGULARITY" = true ]; then
num_pairs=$( wc -l < $tmpfile )
JOB_STAGE2_STEP5_ALTERNATE=$(sbatch --dependency="$JOB_STAGE2_STEP3_PERMUTATION_ALTERNATE_ID" <<EOF
#!/bin/bash
#SBATCH -J phase2_step5_alternate
#SBATCH --array=1-$num_pairs
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step5_alternate_%A_%a.out
threshold=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile | cut -f 1)
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile | cut -f 2)
echo "Threshold \$threshold, Network: \$network"
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_generate_rp_statistics_alternate.py \
--gene_set_path ${OUTPUT_DIR}/RPscores/${TRAITRR}/ \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/master_summary_alternate.csv \
--trait ${TRAITRR} \
--module_path ${OUTPUT_DIR}/${TRAITRR}/enriched_modules/${TRAITRR}-\${network}/ \
--go_path ${OUTPUT_DIR}/${TRAITRR}/GO_summaries_alternate/ \
--output_path ${OUTPUT_DIR}/${TRAITRR}/results/raw_alternate/ \
--network \$network \
--threshold \$threshold
EOF
)
JOB_STAGE2_STEP5_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP5_ALTERNATE" | awk '{print $4}')
else
while IFS=$'\t' read -r threshold network; do
echo "Threshold $threshold, Network: $network"
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_generate_rp_statistics_alternate.py \
--gene_set_path ${OUTPUT_DIR}/RPscores/${TRAITRR}/ \
--master_summary_path ${OUTPUT_DIR}/${TRAITRR}/master_summary_alternate.csv \
--trait ${TRAITRR} \
--module_path ${OUTPUT_DIR}/${TRAITRR}/enriched_modules/${TRAITRR}-${network}/ \
--go_path ${OUTPUT_DIR}/${TRAITRR}/GO_summaries_alternate/ \
--output_path ${OUTPUT_DIR}/${TRAITRR}/results/raw_alternate/ \
--network $network \
--threshold $threshold"
done < $tmpfile
fi
#rm -rf $tmpfile
}
phase2_step6_alternate() {
# (6) summarize statistics from original and permutation runs
echo "# STEP 6: summarize statistics from original and permutation runs"
if [ "$SINGULARITY" = true ]; then
tmpfile=$(mktemp --tmpdir="$(pwd)/tmp")
ls ${MODULEFILEDIR} > $tmpfile
num_networks=$( wc -l < $tmpfile)
JOB_STAGE2_STEP6_ALTERNATE=$(sbatch --dependency=afterok:"$JOB_STAGE2_STEP4_ALTERNATE_ID","$JOB_STAGE2_STEP5_ALTERNATE_ID" <<EOF
#!/bin/bash
#SBATCH -J phase2_step6_alternate
#SBATCH --array=1-$num_networks
#SBATCH --mem-per-cpu=4G
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/phase2_step6_alternate_%A_%a.out
network=\$( sed -n \${SLURM_ARRAY_TASK_ID}p $tmpfile )
network="\${network%.*}" # remove extension
singularity exec --no-home -B $(pwd):$(pwd) --pwd $(pwd) $container_python \
python3 ./scripts/phase2/dc_summary_statistics_rp_alternate.py \
--trait $TRAIT \
--input_path $OUTPUT_DIR \
--or_id $TRAIT \
--rr_id $TRAITRR \
--input_file_rr_id $TRAITRR \
--network \$network \
--output_path ${OUTPUT_DIR}/${TRAIT}/summary_alternate/
EOF
)
JOB_STAGE2_STEP6_ALTERNATE_ID=$(echo "$JOB_STAGE2_STEP6_ALTERNATE" | awk '{print $4}')
else
for network in `ls ${MODULEFILEDIR}/`;
do
echo "Network: $network"
network="${network%.*}" # remove extension
docker run --rm -v $(pwd):$(pwd) -w $(pwd) -u $(id -u):$(id -g) $container_python /bin/bash -c \
"python3 ./scripts/phase2/dc_summary_statistics_rp_alternate.py \
--trait $TRAIT \
--input_path $OUTPUT_DIR \
--or_id $TRAIT \
--rr_id $TRAITRR \
--input_file_rr_id $TRAITRR \
--network $network \
--output_path ${OUTPUT_DIR}/${TRAIT}/summary_alternate/"
done
fi
}
phase2_step7_alternate() {