CHERRY-crispr version

CHERRY is a python library for predicting the interactions between viral and prokaryotic genomes. CHERRY is based on a deep learning model, which consists of a graph convolutional encoder and a link prediction decoder.

In this program, we provide a simplified version of CHERRY, which only used the CRISPRs information in CHERRY's graph for host prediction. In addition, in this lite version, we provide a more easier way to predict the links between bacterial contigs and phage contigs. The sketch of CHERRY-crispr is shown as below:

Input (provided by user):
    1. bacterial contigs from their samples (FASTA files)
    2. phage contigs from their samples (FASTA files)

Output:
    The links (interactions) between bacteria and phages (CSV files)

Required Dependencies

• Python 3.x
• Pandas
• Numpy
• Biopython
• NCBI BLAST+

An easiler way to install

We suggest you to install all the package using conda (both miniconda and Anaconda are ok) following the command lines as below:

conda create --name cherry_crispr python=3.8
conda activate cherry_crispr

conda install pandas numpy biopython

conda install blast -c bioconda

Usage

Once install the required environments, you need to activate it when you want to use:

conda activate cherry_crispr

Then, the commond of CHERRY-crispr can be called by:

python PATH_TO_CHERRY_CRISPR/cherry_crispr.py --bfolder PATH_TO_BACTERIA --pfile PATH_TO_PHAGE --ident IDENTITY_THRESHOLD --threads NUM_OF_THREAD --rootpth PATH_TO_OUTPUT --dbdir PATH_TO_CHERRY_CRISPR/database

OR

python PATH_TO_CHERRY_CRISPR/cherry_crispr.py --bfile PATH_TO_BACTERIA --pfile PATH_TO_PHAGE --ident IDENTITY_THRESHOLD --threads NUM_OF_THREAD --rootpth PATH_TO_OUTPUT --dbdir PATH_TO_CHERRY_CRISPR/database

There are two options for bacterial contigs:

1. --bfolder: the folder where you store your bacterial contigs (all the contigs should be FASTA files)

2. --bfile: the file where you store your bacterial contigs (FASTA file)

For example:

python CHERRY_crispr/cherry_crispr.py --bfolder ~/bacteria/ --pfile ~/phage.fa --threads 40 --rootpth ~/test_dir --dbdir CHERRY_crispr/database

OR

python CHERRY_crispr/cherry_crispr.py --bfile ~/bacteria.fa --pfile ~/phage.fa --threads 40 --rootpth ~/test_dir --dbdir CHERRY_crispr/database

Outputs

There are three output files in --rootpth PATH_TO_OUTPUT.

1. CRISPRs.fa: CRISPRs found in your provided bacteria FASTA
2. crispr_align.txt: BLASTN results between CRISPR and phage
3. cherry_crispr_pred.csv: CSV files of the prediction (alignment > --ident IDENTITY_THRESHOLD)

Citation

If you use this program, please cite the following papers:

• CHERRY:

Jiayu Shang, Yanni Sun, CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model, Briefings in Bioinformatics, 2022;, bbac182, https://doi.org/10.1093/bib/bbac182

• CRT:

Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209

The original version of CHERRY can be found via: CHERRY