## This is a sample PBS script for profiling STR from reference genome using STR-FM
##   
##requirement
##1 STR error rates (can be downloaded from https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files) --> errorrate.bymajorallele
##
echo " "
echo " "
echo "Job started on `hostname` at `date`"
cd /working/directory/
echo ${MOTIF}
echo ${OUTPUT}
echo " "
echo "Generate all possible combination of STR length profile" ## See detail in profilegenerator.xml on https://github.com/Arkarachai/STR-FM
python  profilegenerator.py errorrate.bymajorallele ${MOTIF} 30 > ${OUTPUT}.30

echo "remove duplicated profiles"
cat ${OUTPUT}.30 | sort | uniq > ${OUTPUT}.30.sort

echo "genotyping using error correction model" ## See detail in GenotypingSTR.xml on https://github.com/Arkarachai/STR-FM
python  GenotypeTRcorrection.py  ${OUTPUT}.30.sort errorrate.bymajorallele ${OUTPUT}.30.prob 0.5

echo "select only full motif different --> need to replace 4 with motif size (1-6)"
cat ${OUTPUT}.30.prob | grep  hetero | awk '(($7-$8)==4) || (($8-$7)==4) {print $0}' > ${OUTPUT}.30.prob.screen

echo "Evaluate the probability of the allele combination to generate read profile" ## See detail in  probvalueforhetero.xml on https://github.com/Arkarachai/STR-FM
python heteroprob.py  ${OUTPUT}.30.prob.screen  ${INPUT} >  ${OUTPUT}.30.bino

echo "formatting"
cat  ${OUTPUT}.30.bino | sort  -k 12n,12 -k 6n,6 > ${OUTPUT}.30.bino.sort

echo "Combine read profile probabilities" ## See detail in  combineprobforallelecombination.xml on https://github.com/Arkarachai/STR-FM
python combinedprobforallelecombination.py ${OUTPUT}.30.bino.sort > ${OUTPUT}.30.bino.sort.plot


echo "Job end on `hostname` at `date`"