jasper-vh 2.0

Just a simple virus's hosts predictor

JASPER

JUST A SIMPLE PREDICTOR.

• 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, 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 - Linux
install_dependencies_osx.sh - Mac OS

After that go to JASPER's main directory and:

python setup.py install

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.

Installation summary

You want to have:

• installed jasper python package using setuptools or pip.
• installed each tool and added to PATH

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 a bunch of arguments. A lot of parameters are BLAST parameters and can be configured with JSON file and passed to JASPER. It's also recommended using jasper in empty directory. This ensures, that none of the user's file will be overwritten or damaged. Just do mkdir jasper_results && cd jasper_results and you're good to go.

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 {blast,crispr,trna,mash,wish}.csv --output final_results.csv

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

Output

JASPER produces output in a special format:

The resulting file is a csv file with additional lines that start with # (for easy parsing).

A resulting file is grouped by virus genome. For each viral genome, there are number of Score columns (number of score columns are eq to number of tools used/resulting files merged).

Under each group there is a STD (standard deviation) of that column, which indicates a level of variation. It gives an idea of how much the proposed host are different between each other in a group.

Sample:

Virus	Host	blastScore	crisprScore	mashScore	wishScore
NC_024389	NC_008531	294.0	NaN	0.537086	-1.3626
NC_024389	NC_008531	294.0	NaN	0.537086	-1.3626
NC_024389	NC_017331	NaN	NaN	NaN	-1.35805
# Std		0.0	NaN	0.0	0.002
NC_024391	NC_009641	31180.0	NaN	0.760474	-1.33066
NC_024391	NC_017349	17892.0	NaN	0.789652	-1.32703
NC_024391	NC_017349	17892.0	NaN	0.789652	-1.32703
# Std		6264.023	NaN	0.014	0.002
NC_024392	NC_018586	270.0	28.0	0.484772	-1.36183
NC_024392	NC_021827	270.0	NaN	NaN	-1.36077
NC_024392	NC_021830	270.0	NaN	NaN	-1.3607
NC_024392	NC_021839	270.0	NaN	NaN	-1.36207
NC_024392	NC_021840	270.0	NaN	NaN	-1.35926
NC_024392	NC_017547	74.0	37.0	0.517779	-1.36224
NC_024392	NC_021823	246.0	37.0	0.537086	-1.36111
NC_024392	NC_021823	246.0	37.0	0.537086	-1.36111
NC_024392	NC_010001	NaN	NaN	NaN	-1.34728
# Std		63.37	3.897	0.021	0.004

Std is equal to NaN only when the whole column is equal to NaN which means that there were no results in given tool for given hosts.

Blast config

You can provide blast config as a *.json file. Every module uses a 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