JASPER

JASPER is a free bioinformatics tools for predicting virus hosts. JASPER uses a bunch of bioinformatics tools to prediction virus hosts. It includes genome-genome alignment, CRISPR spacers analyzation, tRNA analyzation and more. JASPER contains few, independent modules blast, crispr, trna, wish, mash, merge.

Requirements

Python 3.7

You need Python >= 3.7 to use JASPER.

Naming convention

Jasper depends on good file naming convention. The best is to use sequence ID as file name, e.x. NC_008876.fna. Software will use this id to name every temp file that needs to be created and also it will use this ID in results file.

WARNING It's not the best idea to use | char in your filename and also in sequence header. Just use normal fasta naming like >NC_00876 additional_info more_additional_info.

If you put multiple contigs in a single file, there is no problem with that. Just be sure that every contig is in it's right file. Jasper repairs every file it read, by default naming it <id from filename>|<#contig> e.x.:

>NC_000856|1
ATGCT....
>NC_000856|2
ATGCA....
# and so on

So even if you have, for instance, one genome in your file, then Jasper will change it's id to <id from filename>|1.

Extensions

Jasper uses input files that ends with [fa, fna, fasta] only!

Additional software

NCBI-Blast+
PILER-CR
WIsH
Mash
tRNAscan-SE

Installation

JASPER uses additional software. It calls every program with subprocess so every program that is stated in above should be installed and added to $PATH.

On Ubuntu:

• To install NCBI-Blast+ use sudo apt install ncbi-blast+
• To install PILER-CR go here, download compiled software, move somewhere and add to $PATH under name pilercr.
• To install tRNAscan-SE go here, download, compile, move somewhere and add to $PATH under name tRNAscan-SE. Remember that tRNAscan-SE needs Infernal to work properly.
• To install WIsH go here, download, compile, move somewhere and add to $PATH under name WIsH.
• To install Mash go here, download release, move somewhere and add to $PATH under name mash.

Source code for additional software:

• NCBI-Blast+: here
• PILER-CR here
• tRNAscan-SE here
• WIsH here
• Mash here

Remember to install everything and add it to path

You can also download the script install_dependencies.sh which will install everything.

After that go to JASPER's main directory and:

python setup.py install

or you can use pip pip3 install jasper-vh or python -m pip install jasper-vh.

PATH

By defaults some pip on linux drops scripts to ~/.local/bin. Add it to your $PATH at the end. export PATH="$HOME/.local/bin:$PATH" Now you're done and you can start using jasper-vh.

Tests

If you want to test, go to proj directory and type python -m unittest discover. It's recommended to do that, since it performs tool check (ensures that user has all dependencies and proper python version).

Usage

JASPER uses bunch of arguments. A lot of parameters are BLAST parameters and can be configured with JSON file and passed to JASPER.

Basic usage

jasper-vh blast --virus path/to/virus/dir --create-db host_db --host /path/to/host/dir --clear
jasper-vh crispr --host path/to/host/dir --create-db vir_db --host /path/to/vir/dir --clear
jasper-vh trna --host path/to/host/dir --virus /path/to/vir/dir --clear
jasper-vh wish --host path/to/host/dir --virus /path/to/vir/dir --clear
jasper-vh mash --host path/to/host/dir --virus /path/to/vir/dir --clear
jasper-vh merge *.csv --output final_results.csv 

For more check --help on jasper individual modules: jasper-vh {blast,crispr,trna,wish,mash,merge} --help

Blast config

You can provide blast config as as a *.json file. Every module uses different task so there are few arguments that are forbidden: ['query', 'db', 'outfmt', 'max_target_seqs', 'num_alignments']

References

• Edgar, R.C. (2007) PILER-CR: fast and accurate identification of CRISPR repeats, BMC Bioinformatics, Jan 20;8:18
• Fichant and Burks, J. Mol. Biol. (1991) Identification of tRNA genes in genomic DNA, 220:659-671.
• Clovis Galiez, Matthias Siebert et al. WIsH: who is the host? Predicting prokaryotichosts from metagenomic phage contigs
• Ondov, B.D., Treangen, T.J., Melsted, P. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016).
• NCBI-BLAST+

License

GPLv3