dfe

Estimating the DFE from the unfolded SNP SFS

I fitted a model with a gamma distributed DFE to the intergenic, intronic, UTR, CDS and 0fold uSFS with 4fold SNPs as reference, as well peaks in these regions, and all peaks together. Mutation rates were assumed to be equal between neutral and selected sites - a requirement to calculate alpha. Runs were bootstrapped 100 times, through resampling with replacement by gene.

0 fold degenerate

mkdir /scratch/project_2002047/sal_enhance/0fold_dfe
cat ../sfs/0fold_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/0fold_dfe/ss_0fold_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/0fold_dfe/*results.txt | python gather_bs_reps.py > salsal31_0fold_gamma-dfe_100bs.csv

CDS regions

mkdir /scratch/project_2002047/sal_enhance/cds_dfe
cat ../sfs/cds_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/cds_dfe/ss_cds_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/cds_dfe/*results.txt | python gather_bs_reps.py > salsal31_cds_gamma-dfe_100bs.csv

UTR

mkdir /scratch/project_2002047/sal_enhance/utr_dfe
cat ../sfs/utr_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/utr_dfe/ss_utr_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/utr_dfe/*results.txt | python gather_bs_reps.py > salsal31_utr_gamma-dfe_100bs.csv

Introns

mkdir /scratch/project_2002047/sal_enhance/intron_dfe 
cat ../sfs/intron_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/intron_dfe/ss_intron_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/intron_dfe/*results.txt | python gather_bs_reps.py > salsal31_intron_gamma-dfe_100bs.csv

Intergenic

mkdir /scratch/project_2002047/sal_enhance/intergenic_dfe 
cat ../sfs/intergenic_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/intergenic_dfe/ss_intergenic_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/intergenic_dfe/*results.txt | python gather_bs_reps.py > salsal31_intergenic_gamma-dfe_100bs.csv

Peaks (all)

mkdir /scratch/project_2002047/sal_enhance/all_enhancers_dfe
cat ../sfs/all_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/all_enhancers_dfe/ss_all-enhancers_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/all_enhancers_dfe/*results.txt | python gather_bs_reps.py > salsal31_all-enhancers_gamma-dfe_100bs.csv

Peaks (0fold)

mkdir /scratch/project_2002047/sal_enhance/0fold_enhancers_dfe  
cat ../sfs/0fold_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/0fold_enhancers_dfe/ss_cds-enhancers_0fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
cd /scratch/project_2002047/sal_enhance/0fold_enhancers_dfe
ls *results.txt | cut -d '_' -f 4-8 | while read i; do mv ss_cds-enhancers_0fold_$i ss_0fold-enhancers_$i; done
cd -
ll /scratch/project_2002047/sal_enhance/0fold_enhancers_dfe/*results.txt | grep -vw 1018 | tr -s ' ' | cut -d ' ' -f 8 | python gather_bs_reps.py > salsal31_0fold-enhancers_gamma-dfe_100bs.csv

Peaks (CDS)

mkdir /scratch/project_2002047/sal_enhance/cds_enhancers_dfe  
cat ../sfs/cds_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/cds_enhancers_dfe/ss_cds-enhancers_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ll /scratch/project_2002047/sal_enhance/cds_enhancers_dfe/*error |  grep -w 0 | tr -s ' ' | cut -d ' ' -f 9 | cut -d '.' -f 1-3 | while read i; do echo $i.results.txt; done | python gather_bs_reps.py > salsal31_cds-enhancers_gamma-dfe_100bs.csv

Peaks (UTR)

mkdir /scratch/project_2002047/sal_enhance/utr_enhancers_dfe 
cat ../sfs/utr_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/utr_enhancers_dfe/ss_utr-enhancers_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ll /scratch/project_2002047/sal_enhance/utr_enhancers_dfe/*error | grep -vw 0 | tr -s ' ' | cut -d ' ' -f 8 | cut -d '.' -f 1-3 | while read i; do sbatch $i.sh; done
ll /scratch/project_2002047/sal_enhance/utr_enhancers_dfe/*error | grep -w 0 | tr -s ' ' | cut -d ' ' -f 8 | cut -d '.' -f 1-3 | while read i; do echo $i.results.txt; done | python gather_bs_reps.py > salsal31_utr-enhancers_gamma-dfe_100bs.csv

Peaks (introns)

mkdir /scratch/project_2002047/sal_enhance/intron_enhancers_dfe 
cat ../sfs/intron_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/intron_enhancers_dfe/ss_intron-enhancers_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/intron_enhancers_dfe/*results.txt | python gather_bs_reps.py > salsal31_intron-enhancers_gamma-dfe_100bs.csv

Peaks (intergenic)

mkdir /scratch/project_2002047/sal_enhance/intergenic_enhancers_dfe 
cat ../sfs/intergenic_enhancers_sfs_data.txt | python enhancer_dfe.py -n 62 -c 1 -dfe continuous -out_pre /scratch/project_2002047/sal_enhance/intergenic_enhancers_dfe/ss_intergenic-enhancers_4fold_continuous_equal_t -constraint equal_mutation_rate -n_search 1000
ls /scratch/project_2002047/sal_enhance/intergenic_enhancers_dfe/*results.txt | python gather_bs_reps.py > salsal31_intergenic-enhancers_gamma-dfe_100bs.csv

Estimated DFEs were binned into selective categories and 95% confidence intervals calculated:

ls salsal31_*_gamma-dfe_100bs.csv | python bin_dfe.py > binned_gammadfe_allregions_nes.csv
Rscript summarise_dfe.R