Separate raw data in groups and updated README.md accordingly

phages/scripts/README.md

@@ -28,7 +28,7 @@ Folders:
 
 * debug
 * lib
-* __pycahce__
+* \_\_pycache\_\_
 
 ----
 
@@ -191,6 +191,8 @@ To run from ipython:
 
 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
 
@@ -215,3 +217,21 @@ 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`

phages/scripts/procedure.sh

-/bin/bash
+#! /bin/bash
+
+
+## SET THE PATH TO THE PHAGES DIRECTORY
+# cd /home/user/work/coev/phages 
+
+
+## PREPARE DATA 
+
+## 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
+
+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
+
+
+
+###################################
+
+