update readme

src/non-b/readme.md

@@ -6,28 +6,28 @@ This repository contains scripts for analyse  non-b dna bed files in order to pl
 
 ### 1. Intersection Script (Bash)
 
-- **Script Name:** `str_intersect_dblbed.sh`
-- **Description:** This Bash script needs two BED files as arguments, then performs a bedtools intersect operation.
+- **Script Name:** `intersect.sh`
+- **Description:** This Bash script needs two BED files as arguments, then performs a bedtools intersect operation to put it in the 3rd argument Path.
 
-### 2. Structural Data Analysis Script (Python)
+### 2. Plotting Density plots (Python)
 
-- **Script Name:** `str_stats.py`
-- **Description:** This Python script reads BED file about non-b dna structures on the human genome, calculates stats about genes and structure length and generate dataframes that can be normalised.
+- **Script Name:** `density_plots.py`
+- **Description:** This python script is made to generate density plot from a community file and a intersect file.
 
-### 3. Plotting Scripts (Python)
+### 3. Plotting Heatmap UPAC composition (Python)
 
-- **Script Name:** `plot_generator.py`
-- **Description:** This Python script contains functions for visualizing the analyzed structural data. It generates density curves and violin plots for each community based on the provided non-b dna structure  and community information.
+- **Script Name:** `heatmap_TF.py`
+- **Description:** This python script is made to generate density plot from a community file and a intersect file.
 
 ## How to Use
 
-the first script takes 2 arguments and need a bedtools environement:
+the first script takes 3 arguments and need a bedtools environement:
 
-str_intersect_dblbed.sh  annotation.bed non-b_structures.bed
+**intersect.sh**  annot.bed file.bed ./paths_to_output
 
-the second script is a fonction script, he is not meant to be used in command line
+the second script generate density plot from an intersect.bed and an community.tsv
 
-the third script call fonction in str_stats.py and plot the dataframes
+the third script generate heatmap of UPAC composition from an intersect.bed and an community.tsv