src/commands.sh: update

src/commands.sh

@@ -779,6 +779,7 @@ mv results/figures/metagene_all_gene_100bin_0_nt-around-0-bin.pdf results/figure
 
 #####################################################
 # Metagene figure of last exons in readthrough genes near (<=2000 nt) or far (> 2000nt) from a CTCF file and last exons from non readthrough genes
+# figures 5C
 #####################################################
 
 # Bed file containing the last exons of expressed gene with readthrough
@@ -834,4 +835,51 @@ for i in ${!list_names[*]}; do
   mv results/figures/metagene_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metaexon_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf
 done
 
-python3 -m src.gc_content -B results/bed_file/readthrough_last_exon_near_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/readthrough_last_exon_far_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/no_readthrough_expressed_last_exon.bed -b readthrough_ctcf readthrough no_readthrough -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 2000
\ No newline at end of file
+
+###########################################################
+# Figures siPP vs siCTRL pour ddx_down_ctcf,
+# , ddx_down figure 5B
+###########################################################
+
+
+list_names=(ddx_down_ctcf ddx_down)
+bed_names=(CTCF_2000_both_ddx_down_with0_exon.bed Far_CTCF_2000_both_ddx_down_with0_exon.bed)
+for i in ${!list_names[*]}; do
+  cname=${list_names[i]}
+  bed=${bed_names[i]}
+  gbed=${bed/exon\.bed/gene-dup.bed}
+  nbed=${gbed/\.bed/}
+  python3 -m src.visu \
+      --design data/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig/ \
+      --region_bed results/bed_file/${gbed} \
+      --region_name ${cname} \
+      --output results/figures/  \
+      --border_name TSS TTS \
+      --environment 10000 25 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin 100 \
+      --norm '0'
+
+  rm results/figures/metagene_${cname}_100bin_10000_nt-around-25-bin_b0_norm.pdf
+
+  python3 -m src.visu \
+      --design data/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig/ \
+      --region_bed results/bed_file/${bed} \
+      --region_name ${cname} \
+      --output results/figures/  \
+      --border_name " " " " \
+      --environment 10000 25 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin 30 \
+      -y 0.15 0.4 \
+      --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+
+  mv results/figures/metagene_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf
+done
+
+python3 -m src.gc_content -B results/bed_file/readthrough_last_exon_near_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/readthrough_last_exon_far_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/no_readthrough_expressed_last_exon.bed -b readthrough_ctcf readthrough no_readthrough -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 2000
+