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Description:

jaspervh 2.0

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