Commit 49794d53 authored by eortega's avatar eortega
Browse files

scripts/README.md all scripts have been described

parent fa2f815a
File mode changed from 100755 to 100644
......@@ -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
```
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