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author | arkarachai-fungtammasan |
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date | Sat, 22 Aug 2015 12:12:35 -0400 |
parents | d5ed5c2e25c3 |
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## 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`"