build-graph

#!/bin/sh

GRAPH=$1
VCFFILE=$2
GRAPHLABELSPREFIX=$3
TESTLABELSPREFIX=$4
MINMAF=$5

GRAPHLABELSFILE=$GRAPHLABELSPREFIX.labels.txt
TESTLABELSFILE=$TESTLABELSPREFIX.labels.txt

## example:
## GRAPH=SCZ8000_CHR1_15
## VCFFILE=SCZ/CHR1.vcf.gz
## GRAPHLABELSFILE=SCZ8000.labels.txt
## TESTLABELSFILE=SCZ1938.labels.txt
## MINMAF=15

## build the graph and train paths
# GRAPH=$1
# LABELSFILE=$2
# VCFFILE=$3
# MINMAF=$4
echo "##########"
echo "########## BUILDING $GRAPH"
echo "##########"
./run-graph-vcf $GRAPH $GRAPHLABELSFILE $VCFFILE $MINMAF

mv $GRAPH.paths.txt.$GRAPHLABELSFILE $GRAPH.paths.txt

## build the test paths on the same graph
# GRAPH=$1
# LABELSFILE=$2
# VCFFILE=$3
echo "##########"
echo "########## BUILDING $GRAPH TEST PATHS"
echo "##########"
./run-graph-vcf-paths $GRAPH $TESTLABELSFILE $VCFFILE

mv $GRAPH.paths.txt.$TESTLABELSFILE $GRAPH.$TESTLABELSPREFIX.paths.txt