Commit c4017642 authored by eortega's avatar eortega
Browse files

Separate raw data in groups and updated README.md accordingly

parent 0b4d4c6c
......@@ -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`
/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
###################################
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