targ_dir='/local/groux/SMILe_seq'
dest_dir='/local/groux/phd_thesis/images/ch_smile-seq'
script_dir='/local/groux/phd_thesis/scripts/ch_smile-seq'

mkdir -p $dest_dir

# Figure 1 from article (SMiLE-seq pipeline)
wget -O $dest_dir/ figure1.jpg https://media.nature.com/lw926/nature-assets/nmeth/journal/v14/n3/images/nmeth.4143-F1.jpg

# HMM figure
cp $targ_dir/SMILe_seq_article/figure_hmm.png $dest_dir/figure_hmm.png

# mix of figure 2B and 3A is taken from my candidacy report 
# results



# recreate figure S4 b
cp $targ_dir/SMILe_seq_results/PWM_evaluation_25000_3/plots/AUC_25000_3_CEBPb.eps $dest_dir/fig_S4b_CEBPb.eps
cp $targ_dir/SMILe_seq_results/PWM_evaluation_25000_3/plots/AUC_25000_3_CTCF.eps  $dest_dir/fig_S4b_CTCF.eps
cp $targ_dir/SMILe_seq_results/PWM_evaluation_25000_3/plots/AUC_25000_3_TCF7.eps  $dest_dir/fig_S4b_TCF7.eps