jasper-vh 1.0.3

Just a simple virus's hosts predictor

JASPER

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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 - not included now, merge.

Requirements

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!

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Additional software

NCBI-Blast+
PILER-CR
tRNAscan-SE # not included in current release

Installation

I will make a simple installation script in my free time.

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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, dowload compiled software, move somwhere and add to $PATH under name pilercr.
• To install tRNAscan-SE use sudo apt install trnascan-se

Source code for additional software:

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

Remember to install everything and add it to path

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.

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.

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
jasper-vh crispr --host path/to/host/dir --create-db vir_db --host /path/to/vir/dir
jasper-vh trna --args # soon
jasper-vh merge results1.csv results2.csv results3.csv [-w --weigths] 0.6 0.2 0.2 --output final_results.csv 

For more check --help on jasper individual modules: jasper-vh {blast,crispr,trna,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.
• NCBI-BLAST+

License

GPLv3