src/commands.sh: change gc content figure -e parameter to 2000 + coverage...

src/commands.sh: change gc content figure -e parameter to 2000 + coverage figure for 5y only on expressed genes

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