scripts/README.md all scripts have been described

phages/scripts/README.md

@@ -151,7 +151,32 @@ No arguments. the path to the file is hard written -- To be corrected
 
 ### 06b_blast_protospaces.sh*
 
+Protospacers come from bacteria, we need to know where do they map on the virus' genome.
 
-* 07_2_run_vcf_parser_all_files.py
-* 07_2_test.py
-* 07_run_vcf_parser_all_files.py*
\ No newline at end of file
+We tried out different parameters, this script is more a reminder of the commands and parameters tested. -- To be corrected
+
+
+## 07_2_run_vcf_parser_all_files.py
+
+This is the current script being used, the previous are old versions, before starting a git.
+
+* 07_2_test.py : 
+* 07_run_vcf_parser_all_files.py*
+
+This is the analysis script.
+It describes the experimental planes to comapare data and make the graphics that were requested: binary and frequency heatmaps.
+It requires the file `vcf_parser3.py` to be located in the same directory.
+
+The analysis is defined in a function in the top of the script.
+
+To run it I use ipython:
+
+```bash
+source ~/envs/coev/bin/activate
+pip install ipython
+```
+
+To run from ipython:
+```
+%run 07_2_run_vcf_parser_all_files.py
+```