cat-classify-SCZ

#!/bin/sh

VCFDIR=SCZ

PREFIX=$1
VCF1=$2
VCF2=$3
MINMAF=$4

GRAPH1="${PREFIX}_${VCF1}_${MINMAF}"
GRAPH2="${PREFIX}_${VCF2}_${MINMAF}"

TRAINLABELS=$PREFIX.train.labels.txt
TESTLABELS=$PREFIX.test.labels.txt

GRAPH="${PREFIX}_${VCF1}+${VCF2}_${MINMAF}"
VCFFILE="$VCFDIR/${VCF1}+${VCF2}.vcf.gz"

## concatenate the two graphs
echo "##########"
echo "########## concatenating $GRAPH1 + $GRAPH2"
echo "##########"
./run-graph-cat $GRAPH $GRAPH1.nodes.txt $GRAPH2.nodes.txt

## build the graph paths
echo "##########"
echo "########## BUILDING $GRAPH TRAIN, TEST, AND COMBINED PATHS"
echo "##########"
./run-graph-vcf-paths $GRAPH $TRAINLABELS $VCFFILE
mv $GRAPH.paths.txt.$TRAINLABELS $GRAPH.train.paths.txt
./run-graph-vcf-paths $GRAPH $TESTLABELS $VCFFILE
mv $GRAPH.paths.txt.$TESTLABELS $GRAPH.test.paths.txt
cat $GRAPH.train.paths.txt $GRAPH.test.paths.txt > $GRAPH.both.paths.txt

## classify the graph using train and test
./classify-graph $GRAPH

## compute PRS on combined paths
./run-graphutils-prs $GRAPH $GRAPH.both 0