build-classify-HLA_PHEWAS

#!/bin/sh

DISEASE=$1
SUFFIX=$2
MAF=$3

## build the graph and training paths
echo "#######################################################"
echo "########## BUILDING GRAPH AND TRAINING PATHS ##########"
echo "#######################################################"
./run-graph-list ${DISEASE} $SUFFIX $MAF
mv HLA_PHEWAS_${DISEASE}_${SUFFIX}.paths.txt.HLA_PHEWAS_${DISEASE}.labels.txt HLA_PHEWAS_${DISEASE}_${SUFFIX}.paths.txt

## build the testing paths
echo "############################################"
echo "########## BUILDING TESTING PATHS ##########"
echo "############################################"
./run-graph-list-paths HLA_PHEWAS_${DISEASE}_${SUFFIX} HLA_PHEWAS_${DISEASE}.testing.labels.txt
mv HLA_PHEWAS_${DISEASE}_${SUFFIX}.paths.txt.HLA_PHEWAS_${DISEASE}.testing.labels.txt HLA_PHEWAS_${DISEASE}_${SUFFIX}.testing.paths.txt

## classify the graph using training and testing
echo "#################################################"
echo "########## CLASSIFYING GRAPH WITH WEKA ##########"
echo "#################################################"
./classify-graph HLA_PHEWAS_${DISEASE}_${SUFFIX}

## build the combined paths for PRS
cat HLA_PHEWAS_${DISEASE}_${SUFFIX}.paths.txt HLA_PHEWAS_${DISEASE}_${SUFFIX}.testing.paths.txt > HLA_PHEWAS_${DISEASE}_${SUFFIX}.both.paths.txt

## compute PRS on combined paths
echo "#####################################################"
echo "########## COMPUTING PRS ON COMBINED PATHS ##########"
echo "#####################################################"
./run-graphutils-prs HLA_PHEWAS_${DISEASE}_${SUFFIX} HLA_PHEWAS_${DISEASE}_${SUFFIX}.both 0