Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs
comparison commandline_sample_STR-FM_estimate_mininum_informative_Read_Depth @ 7:3c05abb4452e default tip
add missing files
author | devteam@galaxyproject.org |
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date | Wed, 22 Apr 2015 12:22:50 -0400 |
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6:dccd7a3ee717 | 7:3c05abb4452e |
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1 ## This is a sample PBS script for profiling STR from reference genome using STR-FM | |
2 ## | |
3 ##requirement | |
4 ##1 STR error rates (can be downloaded from https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files) --> errorrate.bymajorallele | |
5 ## | |
6 echo " " | |
7 echo " " | |
8 echo "Job started on `hostname` at `date`" | |
9 cd /working/directory/ | |
10 echo ${MOTIF} | |
11 echo ${OUTPUT} | |
12 echo " " | |
13 echo "Generate all possible combination of STR length profile" ## See detail in profilegenerator.xml on https://github.com/Arkarachai/STR-FM | |
14 python profilegenerator.py errorrate.bymajorallele ${MOTIF} 30 > ${OUTPUT}.30 | |
15 | |
16 echo "remove duplicated profiles" | |
17 cat ${OUTPUT}.30 | sort | uniq > ${OUTPUT}.30.sort | |
18 | |
19 echo "genotyping using error correction model" ## See detail in GenotypingSTR.xml on https://github.com/Arkarachai/STR-FM | |
20 python GenotypeTRcorrection.py ${OUTPUT}.30.sort errorrate.bymajorallele ${OUTPUT}.30.prob 0.5 | |
21 | |
22 echo "select only full motif different --> need to replace 4 with motif size (1-6)" | |
23 cat ${OUTPUT}.30.prob | grep hetero | awk '(($7-$8)==4) || (($8-$7)==4) {print $0}' > ${OUTPUT}.30.prob.screen | |
24 | |
25 echo "Evaluate the probability of the allele combination to generate read profile" ## See detail in probvalueforhetero.xml on https://github.com/Arkarachai/STR-FM | |
26 python heteroprob.py ${OUTPUT}.30.prob.screen ${INPUT} > ${OUTPUT}.30.bino | |
27 | |
28 echo "formatting" | |
29 cat ${OUTPUT}.30.bino | sort -k 12n,12 -k 6n,6 > ${OUTPUT}.30.bino.sort | |
30 | |
31 echo "Combine read profile probabilities" ## See detail in combineprobforallelecombination.xml on https://github.com/Arkarachai/STR-FM | |
32 python combinedprobforallelecombination.py ${OUTPUT}.30.bino.sort > ${OUTPUT}.30.bino.sort.plot | |
33 | |
34 | |
35 echo "Job end on `hostname` at `date`" |