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view commandline_sample_STR-FM_reference_profiling @ 3:3d58c22ea6c9 draft
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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 version 1.0.0 (April 20, 2014) ## ##requirement ##1 reference genome in FASTA format --> ${INPUT}.fa ## echo " " echo " " echo "Job started on `hostname` at `date`" cd /working/directory/ echo " " echo " detect STR in reference genome" ## See detail in microsatellite.xml on https://github.com/Arkarachai/STR-FM python microsatellite.py ${INPUT}.fa --fasta --period=1 --partialmotifs --minlength=4 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.mono.out python microsatellite.py ${INPUT}.fa --fasta --period=2 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.di.out python microsatellite.py ${INPUT}.fa --fasta --period=3 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.tri.out python microsatellite.py ${INPUT}.fa --fasta --period=4 --partialmotifs --minlength=8 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.tetra.out echo "formatting" cat ${INPUT}.mono.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.mono.TR cat ${INPUT}.di.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.di.TR cat ${INPUT}.tri.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tri.TR cat ${INPUT}.tetra.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tetra.TR echo "Job end on `hostname` at `date`"