diff --git a/phages/scripts/00_create_py_env.sh b/phages/scripts/00_create_py_env.sh
old mode 100644
new mode 100755
index 8612ac94ebcff8f271c99e3dd09c3ffd85c63333..c5743f94046aeba27f2837db696d1305d77ec705
--- a/phages/scripts/00_create_py_env.sh
+++ b/phages/scripts/00_create_py_env.sh
@@ -27,7 +27,7 @@ source  ${py_env_dir}/bin/activate
 pip install --upgrade pip
 
 ## 
-pip install  -r requirements_py-env.txt
+pip install  -r scripts/requirements_py-env.txt
 # pip  install  biopython  pandas   matplotlib  multiqc  pyvcf
 
 
diff --git a/phages/scripts/01_quality_check.sh b/phages/scripts/01_quality_check.sh
index 74ba96742517c97c36aed20f43dbf48e4093c184..cf1fbf67b265e08118bcc02e62b6cd0e74e818ef 100755
--- a/phages/scripts/01_quality_check.sh
+++ b/phages/scripts/01_quality_check.sh
@@ -1,9 +1,14 @@
 #!/bin/bash
 
 
+## Launch example from coevolution/phages/
+## ./scripts/01_quality_check.sh  $PWD/  qc_rawd_data
+
+
 ## PATH TO WORKING DIRECTORY
 path=$1
 #path=/home/enrique/work/Gandon/coevolution/phages/
+step_name=$2
 
 
 
@@ -11,6 +16,9 @@ path=$1
 
 source ~/envs/coev/bin/activate
 
+## Some temporary files are created nearby the source files
+## Using links from a tmp will avoid errors in case the directory
+## containing the raw data is not writable
 
 ## SEPARATE THE FILES BY NAME 
 
@@ -20,47 +28,47 @@ W_seq=$(mktemp -d)
 R_seq=$(mktemp -d)
 Other_seq=$(mktemp -d)
 
-
+echo $W_seq $R_seq $Other_seq
 
 
     ### CREATE SYMBOLIC LINKS TO SEQUENCE FILES
     ### DIIVIDED IN 3 DIRECTORIES
 
-
 echo "CREATE SYMBOLIC LINKS"
 
-for i in $(ls ${path}raw_data/sequences/W*);
+for i in $(ls ${path}data/sequences/W*);
 do
   ln -s $i $W_seq;
 done
 
 
-for i in $(ls ${path}raw_data/sequences/R*);
+for i in $(ls ${path}data/sequences/R*);
 do
   ln -s $i $R_seq;
 done
 
 
-for i in $(ls ${path}raw_data/sequences/ | grep -v ^W | grep -v ^R);
+for i in $(ls ${path}data/sequences/ | grep -v ^W | grep -v ^R);
 do
   #echo $i;
   ln -s ${path}raw_data/sequences/$i $Other_seq
 done
 
 
+echo "CREATE SYMBOLIC LINKS -- DONE"
 
 ### MAKE RUN FASTQC ON EACH GROUPE
 
-mkdir -p ${path}qual/fastqc/{W_seq,R_seq,Other_seq}
+mkdir -p ${path}steps/${step_name}/fastqc/{W_seq,R_seq,Other_seq}
 
 
-fastqc -t 35 --noextract -o ${path}qual/fastqc/W_seq $W_seq/*
+fastqc -t 35 --noextract -o ${path}steps/$step_name/fastqc/W_seq $W_seq/*
 # multiqc -f -i W_seq -o ${path}qual/multiqc/   ${path}qual/fastqc/W_seq 
 
-fastqc -t 35 --noextract -o ${path}qual/fastqc/R_seq $R_seq/*
+fastqc -t 35 --noextract -o ${path}steps/$step_name/fastqc/R_seq $R_seq/*
 # multiqc -f -i R_seq -o ${path}qual/multiqc/ ${path}qual/fastqc/R_seq/
 
-fastqc -t 35 --noextract -o ${path}qual/fastqc/Other_seq $Other_seq/*
+fastqc -t 35 --noextract -o ${path}steps/$step_name/fastqc/Other_seq $Other_seq/*
 # multiqc -f -i Other_seq -o ${path}qual/multiqc/ ${path}qual/fastqc/Other_seq
 
 
@@ -71,17 +79,17 @@ fastqc -t 35 --noextract -o ${path}qual/fastqc/Other_seq $Other_seq/*
 
 ## LOOP MULTIQC DEPENDING ON THE INPUTS
 ## MAKE DIRECTORIES FOR THE DIFFERENT SAMPLES:
-mkdir -p ${path}qual/multiqc/{W,R,Other}
+mkdir -p ${path}steps/$step_name/multiqc/{W_seq,R_seq,Other_seq}
 
 for i in $(seq 8)
 do
-    multiqc -f -i W${i}_seq -n W${i} -o ${path}qual/multiqc/W   ${path}qual/fastqc/W_seq/W${i}*
-    multiqc -f -i R${i}_seq -n R${i} -o ${path}qual/multiqc/R   ${path}qual/fastqc/R_seq/R${i}*
+    multiqc -f -i W${i}_seq -n W${i} -o ${path}steps/$step_name/multiqc/W_seq   ${path}steps/$step_name/fastqc/W_seq/W${i}*
+    multiqc -f -i R${i}_seq -n R${i} -o ${path}steps/$step_name/multiqc/R_seq   ${path}steps/$step_name/fastqc/R_seq/R${i}*
 done
 
 for i in 2972 A B C D CTRL T Undetermined
 do
-    multiqc -f -i ${i}_seq -n ${i} -o ${path}qual/multiqc/Other ${path}qual/fastqc/Other_seq/${i}*
+    multiqc -f -i ${i}_seq -n ${i} -o ${path}steps/$step_name/multiqc/Other_seq  ${path}steps/$step_name/fastqc/Other_seq/${i}*
 done
 
 
diff --git a/phages/scripts/02_trimm_and_clean.sh b/phages/scripts/02_trimm_and_clean.sh
index 9bfb71da40774f491833259feec36cd0b4992a3e..d41f47034e216764791dc6fd0779048406d79e0c 100755
--- a/phages/scripts/02_trimm_and_clean.sh
+++ b/phages/scripts/02_trimm_and_clean.sh
@@ -1,9 +1,14 @@
 #! /bin/bash
 
+## VARIABLES
 
-path=/home/enrique/work/Gandon/coevolution/phages/
+#path=/home/enrique/work/Gandon/coevolution/phages/
+path=$1
+n_threads=35
 
 
+## SCRIPT
+
 mkdir -p data/trimmed/{W_seq,R_seq,Other_seq}
 
 trimm_summary=${path}data/summary_trimm
@@ -45,7 +50,7 @@ do
     echo "Working on file " $shortname;
     java -jar /usr/local/src/Trimmomatic-0.38/trimmomatic-0.38.jar \
         PE \
-        -threads 35 \
+        -threads $n_threads \
         -phred33 \
         -summary /tmp/tmp.trimm_summary \
         -quiet \
@@ -72,7 +77,7 @@ do
     echo "Working on file " $shortname;
     java -jar /usr/local/src/Trimmomatic-0.38/trimmomatic-0.38.jar \
         PE \
-        -threads 35 \
+        -threads $n_threads \
         -phred33 \
         -summary /tmp/tmp.trimm_summary \
         -quiet \
@@ -100,7 +105,7 @@ do
     echo "Working on file " $shortname;
     java -jar /usr/local/src/Trimmomatic-0.38/trimmomatic-0.38.jar \
         PE \
-        -threads 35 \
+        -threads $n_threads \
         -phred33 \
         -summary /tmp/tmp.trimm_summary \
         -quiet \
diff --git a/phages/scripts/03_mapping.sh b/phages/scripts/03_mapping.sh
index 8b78f7155608e6dcb2c5738a678476f67b86d4cd..d32775e4ce11b7759d5476a578bfdcd4a06855e7 100755
--- a/phages/scripts/03_mapping.sh
+++ b/phages/scripts/03_mapping.sh
@@ -2,7 +2,8 @@
 
 
 ## DEFINE PATH
-path=/home/enrique/work/Gandon/coevolution/phages/
+path=$1
+# path=/home/enrique/work/Gandon/coevolution/phages/
 
 
 ## CREATE INDEXES AND 
@@ -13,32 +14,34 @@ path=/home/enrique/work/Gandon/coevolution/phages/
 # bowtie2 --phred33 -5 12 -p 35 -t -x ${path}data/refs/indexes_Sv/Sv -1 ${path}data/trimmed/W_seq/W4T3_S54_R1.fq.gz -2 ${path}data/trimmed/W_seq/W4T3_S54_R2.fq.gz -S ${path}results/test.sam
 
 
-path_fasta=/home/enrique/work/Gandon/coevolution/phages/data/trimmed/
+path_fasta=${path}data/trimmed/
 
-path_results=/home/enrique/work/Gandon/coevolution/phages/results/
+path_results=${path}results/
 
-bacteria_index=/home/enrique/work/Gandon/coevolution/phages/data/refs/indexes_St/St
+bacteria_index=${path}data/refs/indexes_St/St
 
-virus_index=/home/enrique/work/Gandon/coevolution/phages/data/refs/indexes_Sv/Sv
+virus_index=${path}data/refs/indexes_Sv/Sv
 
 
-
-for i in $(find $path_fasta -name *_R1.fq.gz)
+for i in  $(find  $path_fasta  -name *_R1.fq.gz)
 do
+    ## Declare local variables
     # echo $i
-    root_name=$(basename -s _R1.fq.gz $i)
+    root_name=$(basename -s  _R1.fq.gz $i)
     var=$(dirname $i)
     outdir=${var/data\/trimmed/results/mapping}/
 
-    echo -e "\n"phage $root_name -\> ${outdir}${root_name}.sam
-    echo $i ${i/_R1/_R2}
+    ## Give some feedback to the user
+    echo -e  "\n"phage $root_name -\> ${outdir}${root_name}.sam
+    echo $i  ${i/_R1/_R2}
     echo $virus_index
 
+    ## Mapping and indexing bam file
     echo "#### MAPPING"
-    bowtie2 --phred33 -5 12 -p 24 -t -x $virus_index -1 $i -2 ${i/_R1/_R2} -S ${outdir}${root_name}.sam 
+    bowtie2 --phred33  -5 12  -p 24  -t  -x  $virus_index  -1 $i  -2 ${i/_R1/_R2}  -S ${outdir}${root_name}.sam 
 
     echo "#### SORTING"
-    samtools sort -O BAM -o ${outdir}${root_name}.sort.bam ${outdir}${root_name}.sam
-    samtools index -b ${outdir}${root_name}.sort.bam
+    samtools sort  -O BAM  -o ${outdir}${root_name}.sort.bam  ${outdir}${root_name}.sam
+    samtools index  -b ${outdir}${root_name}.sort.bam
 
 done
diff --git a/phages/scripts/04_snpcalling.sh b/phages/scripts/04_snpcalling.sh
index fe9a12193666c6323d580568effc4e315c9a4704..470e1d9a0fa2831d4be035ce422d77647ed69fd4 100755
--- a/phages/scripts/04_snpcalling.sh
+++ b/phages/scripts/04_snpcalling.sh
@@ -3,7 +3,7 @@
 ## SNPCALLING
 
 wd=$1   ## Working directory's path
-ref=$2  ## path to rference.fasta
+ref=$2  ## path to reference.fasta
 od=$3   ## Output directory
 
 
diff --git a/phages/scripts/06b_blast_protospaces.sh b/phages/scripts/06b_blast_protospaces.sh
old mode 100755
new mode 100644
diff --git a/phages/scripts/README.md b/phages/scripts/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..39441b2ce124f21695b0cfac23db399dc954c92f
--- /dev/null
+++ b/phages/scripts/README.md
@@ -0,0 +1,237 @@
+## Contents of scripts folder
+
+The scripts are numbered in the order they are run.
+If in doubt use the scripts which are executable.
+
+A more detailed description of the files is below the list (use ctrl + f)
+
+Files:
+
+* 00_create_py_env.sh
+* 01_quality_check.sh*
+* 02_trimm_and_clean.sh*
+* 03_mapping.sh*
+* 04_snpcalling.sh*
+* 05b_convert_protospacer_dico2fasta.py*
+* 06b_blast_protospaces.sh*
+* 07_2_run_vcf_parser_all_files.py
+* 07_2_test.py
+* 07_run_vcf_parser_all_files.py*
+
+* procedure.sh
+* README.md
+* requirements_py-env.txt
+
+* vcf_parser3.py
+
+Folders:
+
+* debug
+* lib
+* \_\_pycache\_\_
+
+----
+
+## Coding practices
+
+In python I tried to use as much as possible the Python Enhancement Proposal 8 (PEP-8). https://www.python.org/dev/peps/pep-0008/
+
+A difference I use regularly is using double `##` at the begining of a line containing *informative comments*.
+During the developement stages I comment some code lines that would be uncommented as a block. Having two '#' prevents comments to be executed as code.
+
+Example:
+
+```python
+## This block of code calculate the proportion
+for i in input_list:
+    # print("proportion of the list")
+    print(i / sum(list))
+```
+
+Concerning **bash** coding I use often double spaces to separate commands, parameters, and arguments. When using some long names it makes things more readable
+
+Big chunks of code are commented with capitals and short phrases,
+whereas longer phrases in comments are in lower case.
+
+Example:
+
+```bash
+## BIG CODE CHUNK
+
+for i in  $(find  $path_fasta  -name *_R1.fq.gz)
+do
+    ## Declare local variables
+    # echo $i
+    root_name=$(basename -s  _R1.fq.gz $i)
+    var=$(dirname $i)
+    outdir=${var/data\/trimmed/results/mapping}/
+
+    ## Give some feedback to the user
+    echo -e  "\n"phage $root_name -\> ${outdir}${root_name}.sam
+    echo $i  ${i/_R1/_R2}
+    echo $virus_index
+
+    ## Mapping and indexing bam file
+    echo "#### MAPPING"
+    bowtie2 --phred33  -5 12  -p 24  -t  -x  $virus_index  -1 $i  -2 ${i/_R1/_R2}  -S ${outdir}${root_name}.sam 
+
+    echo "#### SORTING"
+    samtools sort  -O BAM  -o ${outdir}${root_name}.sort.bam  ${outdir}${root_name}.sam
+    samtools index  -b ${outdir}${root_name}.sort.bam
+
+done
+```
+
+Sometimes I'll put the arguments in different lines having an indentation:
+
+```bash
+## A command with multiple parameters seaprated per line
+samtools sort  \
+    -O BAM  \
+    -o ${outdir}${root_name}.sort.bam  \
+    ${outdir}${root_name}.sam
+
+## Short commands in one single line
+samtools index  -b ${outdir}${root_name}.sort.bam
+```
+
+----
+
+## File descriptions
+
+
+### 00_create_py_env.sh
+
+Creates a python virtual environment using `virtualenv`, the default python3 version of the system and will storte the environment in `~/envs/coev`. The installation of packages is done through pip.
+
+
+### 01_quality_check.sh*
+
+It will use FastQC to create quality control reports and then use multiqc to assemble the reports in only file. To make things easier, the input files are separated in 3 groups R, W and Other. These groups come from different treatments.
+
+This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke** 
+
+
+### 02_trimm_and_clean.sh*
+
+Launches Trimmomatic to clean data.
+The parameters are embeded in the code -- for now
+
+This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke** 
+
+
+### 03_mapping.sh*
+
+The index creation is commented in the top of the script. It's only required once.
+The path to the input files is a full path using a variable.
+The mapper is bowtie2, after mapping the sam is sorted and converted to a bam and indexed so it's ready for the next stage.
+
+This script takes one argument: The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages/`. **Don't forget that final stroke** 
+
+
+### 04_snpcalling.sh*
+
+It uses freebayes to make the snp calling
+
+This script takes three arguments: 
+1 The path to the working directory, which is the project directory: `/home/user/work/coevolution/phages`. **Don't forget that final stroke** 
+2 Path to the reference
+3 Path to the output directory
+
+
+### 05b_convert_protospacer_dico2fasta.py*
+
+The *protospacer_dico* is a raw text file with only one sequence per line.
+Each line is a protospacer sequence that has been manually selected and curated.
+This script converts these sequences to fasta format.
+The name given to each sequence is the line number.
+
+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.
+
+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 : This is for debuging. The inputs and outputs are in the folder `scripts/debug`
+* 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
+```
+
+----
+
+
+
+## The other scripts
+
+### procedure.sh
+
+The commands used to launch the scripts up here as well as the supplementary commands to separate the different data, extract and all other action is written here.
+
+It contains a pre-treatment of data to create sub-groups using symbolic links.
+
+
+### README.md
+
+This file :-P
+
+
+### requirements_py-env.txt
+
+File used by the script `00_create_py_env.sh`
+It contains the list of libraries and versions used in python for this analysis.
+
+
+### vcf_parser3.py
+
+This is a python library which is imported by `07_2_run_vcf_parser_all_files.py`
+
+It contains allows to import data from vcf files and put it in a pandas dataframe format to ease the analyses.
+
+It works with objects: The _attributes_ contain information and the _methods_ are internal functions for that object. For example "remove control SNPs"
+
+The last class allows to create a heatmap with matplotlib.
+
+A more extended documentation will be made in the future
+
+
+----
+
+## Folders
+
+### debug
+
+Folder to put inputs and outputs for debuging.
+
+### lib
+
+Folder containing the library of some tests,
+toy examples and commands to be called from the other scripts
+
+### * \_\_pycache\_\_
+
+Dispensable.
+Created by python automatically when importing a `*.py`
diff --git a/phages/scripts/procedure.sh b/phages/scripts/procedure.sh
new file mode 100644
index 0000000000000000000000000000000000000000..153f01580c84be500dd9bc73cacd0cac0daed676
--- /dev/null
+++ b/phages/scripts/procedure.sh
@@ -0,0 +1,53 @@
+#! /bin/bash
+
+
+## SET THE PATH TO THE PHAGES DIRECTORY
+# cd /home/user/work/coev/phages 
+
+
+## PREPARE DATA SUBGROUPS
+
+## Uncompress raw data into data folder
+tar -xzvf data/sequences.tar.gz -C data
+
+## Change premissions to avoid accidents
+chmod -w  data/sequences/*
+chmod -w data/sequences.tar.gz
+
+## Make links to data to make sub-groups
+## It makes it easier to handle groups of files
+
+
+## This step is also done on scripts/01_quality_check.sh
+mkdir -p  data/fastq_ln/{R_seq,W_seq,Other_seq}
+
+for i in $PWD/data/sequences/R*
+do
+    ln -s  $i  $PWD/data/fastq_ln/R_seq
+done
+
+
+for i in $PWD/data/sequences/W*
+do
+    ln -s  $i  $PWD/data/fastq_ln/W_seq
+done
+
+
+for i in $(ls raw_data/sequences/  | grep -v -E "^W.*.fastq.gz|^R.*.fastq.gz")
+do
+    ln -s  $PWD/raw_data/sequences/$i  $PWD/data/fastq_ln/Other_seq
+done
+
+
+
+###################################
+## CREATE PYTHON ENVIRONMENT  -- With virtualenv
+
+./scripts/00_create_py_env.sh
+## environment located in:
+## ~/envs/coev/
+
+###################################
+## QUALITY CHECK 
+
+./scripts/01_quality_check.sh  $PWD/  qc_raw_data