From ee75d560b3c9e1209a7e57069d6721fe6b0177b4 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 27 Jan 2021 16:39:01 +0100
Subject: [PATCH] src/commands.sh: change gc content figure -e parameter to
2000 + coverage figure for 5y only on expressed genes
---
src/commands.sh | 31 ++++++++++++++++++++-----------
1 file changed, 20 insertions(+), 11 deletions(-)
diff --git a/src/commands.sh b/src/commands.sh
index 07be5a8..b01d5ac 100644
--- a/src/commands.sh
+++ b/src/commands.sh
@@ -358,7 +358,7 @@ done
############################################################
-python3 -m src.gc_content -B results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed -b ddx_down ddx_down_ctcf -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 1000
+python3 -m src.gc_content -B results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed -b ddx_down ddx_down_ctcf -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 2000
@@ -480,6 +480,7 @@ for i in ${!list_names[*]}; do
--show_replicate n \
--figure_type metagene \
--nb_bin 100 \
+ -y 0.15 0.4 \
--norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
mv results/figures/metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf
@@ -690,6 +691,14 @@ done
# SHY5Y #
##############################
+# Creating a bed file only containing expressed gene in 5y cells
+
+python3 -m src.bed_handler.filter_bed \
+ -b data/bed/gene.bed \
+ -f data/5y_expressed_genes_basemean\>5.txt \
+ -c id \
+ -o 5y_expressed_gene.bed
+
# Create a bed file containing
bins=('None' 0 99)
bin_names=('' '_b0_norm' '_b99_norm')
@@ -697,8 +706,8 @@ for i in ${!bins[@]}; do
python3 -m src.visu \
--design data/bigwig_SHY5Y/design_exp_all_replicates.txt \
--bw_folder data/bigwig_SHY5Y/ \
- --region_bed data/bed/gene.bed \
- --region_name all_gene \
+ --region_bed results/bed_file/5y_expressed_gene.bed \
+ --region_name all_expressed_gene \
--output results/figures/ \
--border_name TSS TTS \
--environment 10000 25 \
@@ -707,11 +716,11 @@ for i in ${!bins[@]}; do
--nb_bin 100 \
--norm ${bins[$i]}
- mv results/figures/metagene_all_gene_100bin_10000_nt-around-25-bin${bin_names[$i]}.pdf results/figures/metagene_5y_rnaseq_all_gene${bin_names[$i]}.pdf
+ mv results/figures/metagene_all_expressed_gene_100bin_10000_nt-around-25-bin${bin_names[$i]}.pdf results/figures/metagene_5y_rnaseq_all_expressed_gene${bin_names[$i]}.pdf
done
tts_sizes=(10000 50000)
-bins=(25 125)
+bins=(25 25)
for i in ${!tts_sizes[@]}; do
size=${tts_sizes[$i]}
bin=${bins[$i]}
@@ -720,26 +729,26 @@ for i in ${!tts_sizes[@]}; do
# Create a bed file containing all gene containing one DDX-down exons
python3 -m src.bed_handler.bed_resize \
- -b data/bed/gene.bed \
+ -b results/bed_file/5y_expressed_gene.bed \
-s ${size} \
-r "end" \
-t "outer" \
- -o all_gene_end${size}.bed
+ -o all_expressed_gene_end${size}.bed
python3 -m src.visu \
--design data/bigwig_SHY5Y/design_exp_all_replicates.txt \
--bw_folder data/bigwig_SHY5Y/ \
- --region_bed results/bed_file/all_gene_end${size}.bed \
- --region_name all_gene \
+ --region_bed results/bed_file/all_expressed_gene_end${size}.bed \
+ --region_name all_expressed_gene \
--output results/figures/ \
--border_name TTS '' \
--environment 0 0 \
--show_replicate n \
--figure_type metagene \
--nb_bin ${bin} \
- --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_gene_100bin_10000_nt-around-25-bin_bin99_norm.txt"
+ --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_5y_expressed_gene_100bin_10000_nt-around-25-bin_bin99_norm.txt"
- mv results/figures/metagene_all_gene_${bin}bin_0_nt-around-0-bin_file_norm.pdf results/figures/metagene_5y_rnaseq_TTS2${kb_size}kb_all_gene_${bin}bin_0_nt-around-0-bin_TTS_norm.pdf
+ mv results/figures/metagene_all_expressed_gene_${bin}bin_0_nt-around-0-bin_file_norm.pdf results/figures/metagene_5y_rnaseq_TTS2${kb_size}kb_expressed_gene_${bin}bin_bin_TTS_norm.pdf
done
--
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