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run_polyDFE.txt
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run_polyDFE.txt
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#################################################################################
######### Running polyDFE on Central Chimpanzee data #########
#################################################################################
#################################################################################
### running analysis using three DFE models:
### full model A: reflected and displaced gamma
### full model C: reflected gamma + exponential
### deleterious model (A or C): reflected gamma
### the deleterious model can be obtained either from model A or C (should yield identical likelihoods)
### each DFE is ran in 4 modes:
### without r, without eps_an
### without r, with eps_an
### with r, without eps_an
### with r, with eps_an
### the 4 modes are controlled through the initialization of the parameters
### given through -i and the provided init files (init_A.txt and init_C.txt)
### to better ensure a global optimum was found,
### 10 basin hopping iterations are used, using -b
#################################################################################
################################################
### Full model A
################################################
### without r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 2 -e > central_chimp_A_nor_noeps
### without r, with eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 3 -e > central_chimp_A_nor
### with r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 4 -e > central_chimp_A_noeps
### with r, with eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 1 -e > central_chimp_A
### to easily enable processing of the results,
### output files can be merged into one file
cat central_chimp_A_nor_noeps > central_chimp_A.txt
cat central_chimp_A_nor >> central_chimp_A.txt
cat central_chimp_A_noeps >> central_chimp_A.txt
cat central_chimp_A >> central_chimp_A.txt
################################################
### Full model C
################################################
### without r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 2 -e > central_chimp_C_nor_noeps
### without r, with eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 3 -e > central_chimp_C_nor
### with r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 4 -e > central_chimp_C_noeps
### with r, with eps_an
### this is the default behavior of polyDFE, so we can skip specifying
### -m C -i init_C.txt 1 -e
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 > central_chimp_C
### merge output
cat central_chimp_C_nor_noeps > central_chimp_C.txt
cat central_chimp_C_nor >> central_chimp_C.txt
cat central_chimp_C_noeps >> central_chimp_C.txt
cat central_chimp_C >> central_chimp_C.txt
################################################
### Deleterious model
################################################
### without r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 6 -e > central_chimp_Del_nor_noeps
### without r, with eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 7 -e > central_chimp_Del_nor
### with r, without eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 8 -e > central_chimp_Del_noeps
### with r, with eps_an
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 5 -e > central_chimp_Del
### merge output
cat central_chimp_Del_nor_noeps > central_chimp_Del.txt
cat central_chimp_Del_nor >> central_chimp_Del.txt
cat central_chimp_Del_noeps >> central_chimp_Del.txt
cat central_chimp_Del >> central_chimp_Del.txt
################################################
### Running without divergence data
################################################
### to not use divergence data, the option -w is used
### full model A
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 2 -e -w > central_chimp_A_nor_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 3 -e -w > central_chimp_A_nor_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 4 -e -w > central_chimp_A_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 1 -e -w > central_chimp_A_no_div
cat central_chimp_A_nor_noeps_no_div > central_chimp_A_no_div.txt
cat central_chimp_A_nor_no_div >> central_chimp_A_no_div.txt
cat central_chimp_A_noeps_no_div >> central_chimp_A_no_div.txt
cat central_chimp_A_no_div >> central_chimp_A_no_div.txt
### full model C
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 2 -e -w > central_chimp_C_nor_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 3 -e -w > central_chimp_C_nor_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m C -i init_C.txt 4 -e -w > central_chimp_C_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -w > central_chimp_C_no_div
cat central_chimp_C_nor_noeps_no_div > central_chimp_C_no_div.txt
cat central_chimp_C_nor_no_div >> central_chimp_C_no_div.txt
cat central_chimp_C_noeps_no_div >> central_chimp_C_no_div.txt
cat central_chimp_C_no_div >> central_chimp_C_no_div.txt
### deleterious model
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 6 -e -w > central_chimp_Del_nor_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 7 -e -w > central_chimp_Del_nor_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 8 -e -w > central_chimp_Del_noeps_no_div
./polyDFE -d central_chimp_sfs -b params_basinhop.txt 1 -m A -i init_A.txt 5 -e -w > central_chimp_Del_no_div
cat central_chimp_Del_nor_noeps_no_div > central_chimp_Del_no_div.txt
cat central_chimp_Del_nor_no_div >> central_chimp_Del_no_div.txt
cat central_chimp_Del_noeps_no_div >> central_chimp_Del_no_div.txt
cat central_chimp_Del_no_div >> central_chimp_Del_no_div.txt