Analysis of interaction between SARS-CoV-2 sequence variation and predicted HLA binding

set up

Python is a coding language that is great because it is quite readable, and pretty easy to get started with. One of the things about Python is that there are a lot of existing packages -- this means we don't have to reinvent the wheels super often. There are also a variety of tools that allow for efficient management of packages. This means we can control 1) which version of Python we're using, 2) which version of packages we're using, 3) install everything at once.

For package management, I use Miniconda. Go to this link to install Miniconda for MacOSX: https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html

Essentially, you can just follow these steps:

Open Terminal app.
If you haven't done any coding before, it'll be helpful for you to run this command:

xcode-select --install

Copy paste the following commands.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh $HOME/miniconda

I think the installer should ask “Do you wish the installer to initialize Miniconda3 by running conda init?” and you should answer yes.

I'm pretty you should be good after this. I think in your terminal window, you can enter the command

python

and I hope you can see something like the following output:

Python 2.7.16 |Anaconda, Inc.| (default, Aug 13 2019, 12:00:15) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

The important part here is that you see something like "Anaconda, Inc.| (default, Aug 13 2019, 12:00:15) " after Python <version number>.

Next, we're going to talk about setting up our Conda environment.

conda environments

So the first step is actually to set up github. Because you have a .edu email, you can get a free Github Pro account: https://education.github.com/pack

After you've made an account, you can go to this link and follow the instructions: https://kbroman.org/github_tutorial/pages/first_time.html

Now that Github is set up, you want to clone (basically, download) this repository. You can do this by doing the following:

cd 
cd Documents/
git clone https://github.com/alexluuuu/covid_analysis.git

Feel free to change the cd command to put the cloned repo into a different directory.

Note that there is an file called environment.yml in this repository. It contains the name of a local environment that we will be using, and which packages should be included in this environment. To initialize a local env based on this configuration file, do the following:

cd covid_analysis
conda env create -f environment.yml

If prompted about the installation of packages, enter "y".

If we ever need to update this conda environment, we'll make change the list of packages in the environment.yml file and run the following command:

conda env update --prefix ./env --file environment.yml  --prune

You can activate the local environment by doing:

conda activate bioinformatics

You can deactivate the local environment by doing:

conda deactivate

It would be best if you activate the local environment whenever we're working on code

It's probably helpful for you to read the following: https://medium.com/crowdbotics/a-dead-simple-intro-to-github-for-the-non-technical-f9d56410a856

I will continue to push changes to this repository over the next few days, so you might want to pull them (sync down from repository in cloud to your local machine).

Getting started on some code

Here's the official Python tutorial: https://docs.python.org/3/tutorial/introduction.html

I feel like you can jump to Chapter 3, but if you want to be really thorough, Ch1-2 should be good too.

I've also attached a starter code file starter.py. I've attached a lot of explanations in that file for how things work.

Commands for the cluster

sbatch -c 2 -t 4:0:0 -p shared --mail-type=begin --mail-type=end --mail-user=alu27@jhu.edu --job-name=matlab

PARAMETER            DEFAULT VALUE        DESCRIPTION
[-a filename]        HLA-A0201            HLA allele name
[-f filename]                             Input file (by default in FASTA format)
[-p]                 0                    Switch on if input is a list of peptides (Peptide format)
[-l string]          9                    Peptide length (multiple lengths separated by comma e.g. 8,9,10)
[-s]                 0                    Sort output on decreasing affinity
[-rth float]         0.500000             Threshold for high binding peptides (%Rank)
[-rlt float]         2.000000             Threshold for low binding peptides (%Rank)
[-listMHC]           0                    Print list of alleles included in netMHC
[-xls]               0                    Save output to xls file
[-xlsfile filename]  NetMHC_out.xls       File name for xls output
[-t float]           -99.900002           Threshold for output
[-thrfmt filename]   $NETMHC/data/threshold/%s.thr Format for threshold filenames
[-hlalist filename]  $NETMHC/data/allelelist File with covered HLA names
[-rdir filename]     $NETMHC              Home directory for NetMHC
[-tdir filename]     $TMPDIR              Temporary directory (Default $$)
[-syn filename]      $NETMHC/data/synlists/%s.synlist Format of synlist file
[-v]                 0                    Verbose mode
[-dirty]             0                    Dirty mode, leave tmp dir+files
[-inptype int]       0                    Input type [0] FASTA [1] Peptide
[-version filename]  $NETMHC/data/version File with version information
[-w]                 0                    w option for webface