#!/bin/sh

checkExitCode() {
if [ $? -ne 0 ]; then
	echo "Error"
	exit 1;
fi
}

BASEDIR=`dirname $0`

if [ $# -lt 1 ]; then echo "Error No inputs provided" && exit 1; fi

. $BASEDIR/io.sh 3 0 1 "$@"

# Edit any special characters- for now second-">" (rash) in the input FASTA files before concatenating them

sed -i -e "s/>/_/2" ${INPUTS1}
sed -i -e "s/>/_/2" ${INPUTS2}
sed -i -e "s/>/_/2" ${INPUTS3}

# Do not include proteins which overlap between *rpkm.fasta and snv fasta file or *rpkm and indel fasta files
# Call the python script to filter and concatenate files.
# Join snv and indel files before calling the python script
INPUTS1_2=`basename $INPUTS1`_`basename $INPUTS2`
echo $INPUTS1_2
# Issues with indel fasta file. can ignore for now. Zhang doesn't use indels
cat $INPUTS1 > $INPUTS1_2
#cat $INPUTS1 $INPUTS2 > $INPUTS1_2

# Hardcoding python location for now
/usr/bin/python $BASEDIR/filterJoinProtFasta.py -1 ${INPUTS1_2} -2 ${INPUTS3} -o ${OUTPUTS1}
#cat $INPUTS1 $INPUTS2 $INPUTS3 > $OUTPUTS1
checkExitCode