src/commands.sh: removing genes with readthrough/no readthrough with a basemean <= 5

src/commands.sh

@@ -574,21 +574,25 @@ mv results/figures/metagene_all_ddx_down_100bin_10000_nt-around-25-bin.pdf resul
 python3 -m src.bed_handler.filter_bed -b data/bed/gene.bed -f data/readthrough_gene.txt -c score -o readthrough_gene.bed
 python3 -m src.bed_handler.filter_bed -b data/bed/gene.bed -f data/readthrough_gene.txt -c score -o no_readthrough_gene.bed -k 'n'
 
+# Filtering only expressed genes with basemean > 5.
+python3 -m src.bed_handler.filter_bed -b results/bed_file/readthrough_gene.bed -f data/5y_expressed_genes_basemean\>5.txt -c id -o readthrough_expressed_gene.bed
+python3 -m src.bed_handler.filter_bed -b results/bed_file/no_readthrough_gene.bed -f data/5y_expressed_genes_basemean\>5.txt -c id -o no_readthrough_expressed_gene.bed
+
 
 # Create bed file corresponding to the 10kb downstream regions of the previous beds
 python3 -m src.bed_handler.bed_resize \
-  -b results/bed_file/no_readthrough_gene.bed \
+  -b results/bed_file/no_readthrough_expressed_gene.bed  \
   -s 10000 \
   -r "end" \
   -t "outer" \
-  -o no_readthrough_gene_10kb.bed
+  -o no_readthrough_expressed_gene_10kb.bed
 
 python3 -m src.bed_handler.bed_resize \
--b results/bed_file/readthrough_gene.bed \
+-b results/bed_file/readthrough_expressed_gene.bed \
 -s 10000 \
 -r "end" \
 -t "outer" \
--o readthrough_gene_10kb.bed
+-o readthrough_expressed_gene_10kb.bed
 
 
 exps=(all_replicates siCTRL siDDX)
@@ -598,7 +602,7 @@ for exp in ${exps[*]}; do
     python3 -m src.visu \
         --design data/design_exp_${exp}.txt \
         --bw_folder data/bigwig/ \
-        --region_bed results/bed_file/readthrough_gene.bed results/bed_file/no_readthrough_gene.bed \
+        --region_bed results/bed_file/readthrough_expressed_gene.bed results/bed_file/no_readthrough_expressed_gene.bed \
         --region_name readthrough no_readthrough \
         --output results/figures/  \
         --border_name TSS TTS \
@@ -621,7 +625,7 @@ for exp in ${exps[*]}; do
     python3 -m src.visu \
         --design data/design_exp_${exp}.txt \
         --bw_folder data/bigwig/ \
-        --region_bed results/bed_file/readthrough_gene_10kb.bed results/bed_file/no_readthrough_gene_10kb.bed \
+        --region_bed results/bed_file/readthrough_expressed_gene_10kb.bed results/bed_file/no_readthrough_expressed_gene_10kb.bed \
         --region_name readthrough no_readthrough \
         --output results/figures/  \
         --border_name TTS '' \
@@ -629,9 +633,9 @@ for exp in ${exps[*]}; do
         --show_replicate n \
         --figure_type metagene \
         --nb_bin 25 \
-        --norm "results/figures/coef_table/tmp_cov_table_design_exp_${exp}_readthrough_gene-no_readthrough_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
+        --norm "results/figures/coef_table/tmp_cov_table_design_exp_${exp}_readthrough_expressed_gene-no_readthrough_expressed_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
 
-    mv results/figures/metagene_readthrough-no_readthrough_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/${exp}_TTS10kb_metagene_readthrough-no_readthrough_25bin_0_nt-around-0-${loc[$i]}_norm.pdf
+    mv results/figures/metagene_readthrough-no_readthrough_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/${exp}_TTS10kb_readthrough-no_readthrough_${loc[$i]}_norm.pdf
   done
 done
 
@@ -643,7 +647,7 @@ for bed in ${beds[*]}; do
     python3 -m src.visu \
         --design data/design_exp_all_replicates.txt \
         --bw_folder data/bigwig/ \
-        --region_bed results/bed_file/${bed}_gene.bed \
+        --region_bed results/bed_file/${bed}_expressed_gene.bed \
         --region_name ${bed} \
         --output results/figures/  \
         --border_name TSS TTS \
@@ -653,7 +657,7 @@ for bed in ${beds[*]}; do
         --nb_bin 100 \
         --norm ${bin}
 
-    mv results/figures/metagene_${bed}_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/all_replicates_metagene_${bed}_25bin_10000_nt-around-25-bin_b${bin}_norm.pdf
+    mv results/figures/metagene_${bed}_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/all_replicates_${bed}_b${bin}_norm.pdf
   done
 done
 
@@ -666,7 +670,7 @@ for bed in ${beds[*]}; do
     python3 -m src.visu \
           --design data/design_exp_all_replicates.txt \
           --bw_folder data/bigwig/ \
-          --region_bed results/bed_file/${bed}_gene_10kb.bed \
+          --region_bed results/bed_file/${bed}_expressed_gene_10kb.bed \
           --region_name ${bed} \
           --output results/figures/  \
           --border_name TTS '' \
@@ -674,9 +678,9 @@ for bed in ${beds[*]}; do
           --show_replicate n \
           --figure_type metagene \
           --nb_bin 25 \
-          --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${bed}_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
+          --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${bed}_expressed_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
 
-    mv results/figures/metagene_${bed}_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/metagene_TTS210kb_${bed}_25bin_0_nt-around-0-${loc[$i]}-bin_norm.pdf
+    mv results/figures/metagene_${bed}_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/all_replicates_TTS10kb_${bed}_${loc[$i]}-bin_norm.pdf
   done
 done