Mercurial > repos > arkarachai-fungtammasan > str_fm
comparison commandline_sample_STR-FM_reference_profiling @ 2:d5ed5c2e25c3 draft
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| author | arkarachai-fungtammasan |
|---|---|
| date | Wed, 22 Apr 2015 12:48:40 -0400 |
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| children |
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| 1:f2bab38e3cbd | 2:d5ed5c2e25c3 |
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| 1 ## This is a sample PBS script for profiling STR from reference genome using STR-FM version 1.0.0 (April 20, 2014) | |
| 2 ## | |
| 3 ##requirement | |
| 4 ##1 reference genome in FASTA format --> ${INPUT}.fa | |
| 5 ## | |
| 6 echo " " | |
| 7 echo " " | |
| 8 echo "Job started on `hostname` at `date`" | |
| 9 cd /working/directory/ | |
| 10 echo " " | |
| 11 echo " detect STR in reference genome" ## See detail in microsatellite.xml on https://github.com/Arkarachai/STR-FM | |
| 12 python microsatellite.py ${INPUT}.fa --fasta --period=1 --partialmotifs --minlength=4 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.mono.out | |
| 13 python microsatellite.py ${INPUT}.fa --fasta --period=2 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.di.out | |
| 14 python microsatellite.py ${INPUT}.fa --fasta --period=3 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.tri.out | |
| 15 python microsatellite.py ${INPUT}.fa --fasta --period=4 --partialmotifs --minlength=8 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0 --splitbyvalidity >${INPUT}.tetra.out | |
| 16 | |
| 17 echo "formatting" | |
| 18 cat ${INPUT}.mono.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.mono.TR | |
| 19 cat ${INPUT}.di.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.di.TR | |
| 20 cat ${INPUT}.tri.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tri.TR | |
| 21 cat ${INPUT}.tetra.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tetra.TR | |
| 22 | |
| 23 | |
| 24 | |
| 25 echo "Job end on `hostname` at `date`" |