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comparison commandline_sample_STR-FM_reference_profiling @ 7:3c05abb4452e default tip

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author devteam@galaxyproject.org
date Wed, 22 Apr 2015 12:22:50 -0400
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6:dccd7a3ee717 7:3c05abb4452e
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
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25 echo "Job end on `hostname` at `date`"