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Commit 75a415a8 authored by nfontrod's avatar nfontrod
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src/commands.sh: update Figures 1C, figures 5C and 5B to use the new bigwig files

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with 53 additions and 42 deletions
src/commands.sh
+ 53
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......@@ -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
......
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