# Using PRESCOTT via Docker

## Requirements

You need to have docker installed on your machine. You can consult the following page for this: https://docs.docker.com/get-docker/

I am assuming some basic familiarity with Linux/Unix/MacOS terminal commands.

Let’s start our favorite terminal app.

You must create a folder called docker-tutorial and go to that empty folder:

    mkdir docker-tutorial
    cd docker-tutorial

## Getting the example input data

Let’s download the sample data provided in the PRESCOTT repository for this exercise. First, we will download the multiple sequence alignment file in fasta format:

    wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta

If you don’t have wget, you can try the same command with curl:

    curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta

Please verify that the aliBLAT.fasta file is in the folder.

Now, we will download the PDB (Protein Databank) file for BLAT:

    wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb

## Single point mutation calculations

In order to make sure that the docker is installed:

    sudo docker -h

If it shows you a list of options, you are on a good track. On MacOS, you may not need ‘sudo’ word before the docker command at all.

    sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
    tekpinar/esgemme-docker:v1.4.0

You are in the container (your virtual operating system) now. You created a folder called myexample in your container with the previous command. Let’s change to that folder.

    cd ../myexample/

When you check the data in that folder with ‘ls’ command, you are supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your docker-tutorial folder on the host system and myexample folder on the docker container are pointing to the same place.

### Obtaining the entire single point mutation landscape

In this step, we will use only evolutionary information from an MSA file:

    esgemme aliBLAT.fasta -f aliBLAT.fasta

After a few minutes of calculation, you must see at least two files named BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have the entire single point mutational landscape of BLAT protein in these files.

If you want to utilize structural information (highly recommended) as well as evolutionary information:

    esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb

### Predicting the effect of a subset of single point mutations

If you are interested in only a bunch of single point mutations, you have to prepare a mut file. The format is a simple text file and each line contains a single point mutation such as D26A…. Fortunately, we have an example mut in data folder of PRESCOTT repository.

    wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut

Similar to the previous step, there are two possible ways to do the calculations: with or without structural information. First, let’s do it without structural information:

    esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut

You can include structural information in the following way:

    esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
    -m Stiffler_2015_BLAT_ECOLX.mut

You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output format is completely different from the entire mutational landscape scanning file. Each line of this file is a mutation and its predicted effect separated by a space. In addition, you won’t have a png file like in the previous case.

## Multiple point mutation calculations

Sometimes, we need to see effects of double or triple mutations. PRESCOTT can perform calculations if you provide a mut file. In this case, the mut file must have the following format:

    E26D:Y44R
    E56N:A77F:H94V

The first line of the text file is impact of a double mutation and the second line is the impact of the triple mutations. As you can see, the mutations are separated by a colon(:) character. The output file will be in a similar format. Each line will contain the multiple mutation and its predicted effect, separated by a space.

## Running several jobs using docker