From 75a415a8f930aa8b7fe6068060b9c56e12b89419 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 21 Feb 2022 09:30:37 +0100
Subject: [PATCH] src/commands.sh: update Figures 1C, figures 5C and 5B to use
the new bigwig files
---
src/commands.sh | 95 +++++++++++++++++++++++++++----------------------
1 file changed, 53 insertions(+), 42 deletions(-)
diff --git a/src/commands.sh b/src/commands.sh
index 3462df0..88c0e04 100644
--- a/src/commands.sh
+++ b/src/commands.sh
@@ -641,47 +641,56 @@ for exp in ${exps[*]}; do
done
-bins=(0 99)
-beds=(readthrough no_readthrough)
+# Figure 1C
+names=(IP)
+designs=(data/designnew_exp_all_replicates_IP.txt)
+bins=(99) # 0)
+beds=(readthrough) # no_readthrough)
for bed in ${beds[*]}; do
for bin in ${bins[*]}; do
- python3 -m src.visu \
- --design data/design_exp_all_replicates.txt \
- --bw_folder data/bigwig/ \
- --region_bed results/bed_file/${bed}_expressed_gene.bed \
- --region_name ${bed} \
- --output results/figures/ \
- --border_name TSS TTS \
- --environment 10000 25 \
- --show_replicate n \
- --figure_type metagene \
- --nb_bin 100 \
- --norm ${bin}
+ for i in ${!designs[@]}; do
+ python3 -m src.visu \
+ --design ${designs[i]} \
+ --bw_folder data/bigwig_newnorm/ \
+ --region_bed results/bed_file/${bed}_expressed_gene.bed \
+ --region_name ${bed} \
+ --output results/figures/ \
+ --border_name TSS TTS \
+ --environment 10000 25 \
+ --show_replicate n \
+ --figure_type metagene \
+ --nb_bin 100 \
+ --norm ${bin}
- mv results/figures/metagene_${bed}_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/all_replicates_${bed}_b${bin}_norm.pdf
+ mv results/figures/metagene_${bed}_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/Fig1C_${bed}_b${bin}_norm_${names[$i]}.pdf
+ done
done
done
-beds=(readthrough no_readthrough)
-bins=(0 99)
-loc=(TSS TTS)
+names=(IP)
+designs=(data/designnew_exp_all_replicates_IP.txt)
+beds=(readthrough) # no_readthrough)
+bins=(99) # 0)
+loc=(TTS) # TSS)
for bed in ${beds[*]}; do
for i in ${!bins[@]}; do
- python3 -m src.visu \
- --design data/design_exp_all_replicates.txt \
- --bw_folder data/bigwig/ \
- --region_bed results/bed_file/${bed}_expressed_gene_10kb.bed \
- --region_name ${bed} \
- --output results/figures/ \
- --border_name TTS '' \
- --environment 0 0 \
- --show_replicate n \
- --figure_type metagene \
- --nb_bin 25 \
- --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${bed}_expressed_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
-
- mv results/figures/metagene_${bed}_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/all_replicates_TTS10kb_${bed}_${loc[$i]}-bin_norm.pdf
+ for j in ${!designs[@]}; do
+ python3 -m src.visu \
+ --design ${designs[i]} \
+ --bw_folder data/bigwig_newnorm/ \
+ --region_bed results/bed_file/${bed}_expressed_gene_10kb.bed \
+ --region_name ${bed} \
+ --output results/figures/ \
+ --border_name TTS '' \
+ --environment 0 0 \
+ --show_replicate n \
+ --figure_type metagene \
+ --nb_bin 25 \
+ --norm "results/figures/coef_table/tmp_cov_table_designnew_exp_all_replicates_${names[$j]}_${bed}_expressed_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
+
+ mv results/figures/metagene_${bed}_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/Fig_1C_TTS10kb_${bed}_${loc[$i]}-bin_norm_${names[$j]}.pdf
+ done
done
done
@@ -804,8 +813,8 @@ for i in ${!list_names[*]}; do
gbed=${bed/exon\.bed/gene-dup.bed}
nbed=${gbed/\.bed/}
python3 -m src.visu \
- --design data/design_exp_all_replicates.txt \
- --bw_folder data/bigwig/ \
+ --design data/designnew_exp_all_replicates_IP.txt \
+ --bw_folder data/bigwig_newnorm \
--region_bed results/bed_file/${gbed} \
--region_name ${cname} \
--output results/figures/ \
@@ -819,8 +828,8 @@ for i in ${!list_names[*]}; do
rm results/figures/metagene_${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/ \
+ --design data/designnew_exp_all_replicates_IP.txt \
+ --bw_folder data/bigwig_newnorm \
--region_bed results/bed_file/${bed} \
--region_name ${cname} \
--output results/figures/ \
@@ -829,8 +838,9 @@ for i in ${!list_names[*]}; do
--show_replicate n \
--figure_type metagene \
--nb_bin 30 \
+ --stat True \
-y 0.15 0.4 \
- --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+ --norm "results/figures/coef_table/tmp_cov_table_designnew_exp_all_replicates_IP_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
mv results/figures/metagene_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metaexon_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf
done
@@ -850,8 +860,8 @@ for i in ${!list_names[*]}; do
gbed=${bed/exon\.bed/gene-dup.bed}
nbed=${gbed/\.bed/}
python3 -m src.visu \
- --design data/design_exp_all_replicates.txt \
- --bw_folder data/bigwig/ \
+ --design data/designnew_exp_all_replicates_IP.txt \
+ --bw_folder data/bigwig_newnorm/ \
--region_bed results/bed_file/${gbed} \
--region_name ${cname} \
--output results/figures/ \
@@ -865,8 +875,8 @@ for i in ${!list_names[*]}; do
rm results/figures/metagene_${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/ \
+ --design data/designnew_exp_all_replicates_IP.txt \
+ --bw_folder data/bigwig_newnorm/ \
--region_bed results/bed_file/${bed} \
--region_name ${cname} \
--output results/figures/ \
@@ -876,7 +886,8 @@ for i in ${!list_names[*]}; do
--figure_type metagene \
--nb_bin 30 \
-y 0.15 0.4 \
- --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+ --stat True \
+ --norm "results/figures/coef_table/tmp_cov_table_designnew_exp_all_replicates_IP_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
mv results/figures/metagene_${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
--
GitLab