autocbei

unittest

We provided command-line versions that can be used to design the cytosine base editor mediated gene inactivation for large amounts of CDS.

We developed the 'autocbei' to automate the calculation of potential CBEI loci of the target CDSs and to perform statistics and calculations.

1. Install

"autocbei" relies on python3 and requires 'biopython' and 'matplotlib' packages. The current version (1.6.3) supports ‘conda’ and ‘pip’ installations.

1.1 Install by conda (Recommended)

Conda (including Anaconda and Miniconda) is a popular way to manage software. It can create and configure a virtual environment without affecting global settings.

First install the corresponding platform of Anaconda or Miniconda. We recommend installing python3 version.

Then execute the following command:

        # Creating a virtual environment of python3.7.
        1. conda create -n runCBEI python=3.7 -y
        # Activate the environment
        2. conda activate runCBEI
        # Install autocbei
        3. conda install -c atlasbioinfo autocbei -y

1.2 Install by pip

If Python3 (Python >= 3.6.0) is already included in your operating system, autocbei can be automatically installed via pip.

pip install autocbei

If you haven't installed python3 yet, it's recommended to use the 'method 1.1' above.

If you want to try out the latest but unreleased version (possibly unstable) of autocbei, please follow these commands:

        # Download CRISPR-CBEI from Github
        1. git clone https://github.com/atlasbioinfo/CRISPR-CBEI.git        
        # Install biopython and matplotlib
        2. conda install -y biopython matplotlib 
        # Run autocbei and show help info
        3. python run_autocbei.py -h

2 Usage

2.1 Demo CDS file

If the installation of "autocbei" has been successful, the sample file is located at [PYTHONHOME]/site-packages/autocbei/Bacillussubtilis.part500.cds.all.fa

If installed with Conda, it should be located at:

~/anaconda3/envs/autocbei/lib/python3.7/site-packages/autocbei/Bacillus_subtilis.part500.cds.all.fa

Or, it can be downloaded via "https://github.com/atlasbioinfo/CRISPR-CBEI/blob/master/autocbei/Bacillus_subtilis.part500.cds.all.fa".

2.2 Run

The -h parameter shows help information.

autocbei -h

        usage: autocbei [-h] [-ns] [-o OUTPREFIX] CDS.fasta
        Enter fasta file of CDSs, output base editor's potential editing site and
        statistics information. The demo CDS Fasta file: "[PATHON_HOME]/site-
        packages/autocbei/Bacillus_subtilis.part500.cds.all.fa".
        positional arguments:
        CDS.fasta             CDSs in fasta format.
        optional arguments:
        -h, --help            show this help message and exit
        -ns, --nostat         Only run CBEI design without statistics and plot.
        -o OUTPREFIX, --outprefix OUTPREFIX
                                Directory prefixes can be customized. Default: "CBEI"
                                (CBEIRaw, CBEIPlot, CBEIRes).

Calculate the potential CRISPR base editing site information of CDSs

autocbei Bacillus_subtilis.part500.cds.all.fa

Calculation only without statistics and ploting:

autocbei -ns Bacillus_subtilis.part500.cds.all.fa -o Bac

3. Base editors

The autoCBEI contains 13 commonly used base editors.

#Set the Base editor parameter
# [PAM, spacer length, edit beg, edit end, direction]
# Direction refers to spacer at the 5' or 3' end of PAM sequence (5 or 3, respectively).
beinfos = {
    "BE":["NGG",20,4,8,5],
    "YE1-BE3":["NGG",20,5,7,5],
    "EE-BE3":["NGG",20,5,6,5],
    "YEE-BE3":["NGG",20,6,6,5],
    "VQR-BE3":["NGAN",20,4,11,5],
    "VRER-BE3":["NGCG",20,3,10,5],
    "SaBE":["NNGRRT",21,3,12,5],
    "Sa(KKH)-BE3":["NNNRRT",21,3,12,5],
    "Cas12a–BE":["TTTV",20,10,12,3],
    "Target-AID":["NGG",20,2,4,5],
    "Target-AID-NG":["NG",20,2,4,5],
    "xBE3":["NG",20,4,8,5],
    "BE-PLUS":["NGG",20,4,14,5]
    # Or, add your own Base editors
    # "BE name" :[PAM, SpLength, EditBeg, EditEnd, Direction]
}

PAM: PAM sequence.

SpLength: Spacer length.

EditBeg: Edit windows begin.

EditEnd: Edit windows end.

Direction: 5 or 3. Spacer is at the 5 'end or 3' end of the PAM sequence. The example in the figure is the 5.