find antimcirobial resistance genes on genomes
Project description
ResBlaster
____ ____ _ _
| _ \ ___ ___| __ )| | __ _ ___| |_ ___ _ __
| |_) / _ \/ __| _ \| |/ _` / __| __/ _ \ '__|
| _ < __/\__ \ |_) | | (_| \__ \ || __/ |
|_| \_\___||___/____/|_|\__,_|___/\__\___|_|
Installation
pip3 install ResBlaster
Dependency
-
BLAST+ >2.7.0
-
cvmblaster (v0.4.1)
you should add BLAST in your PATH
Blast installation
Windows
Following this tutorial: Add blast into your windows PATH
Linux/Mac
The easyest way to install blast is:
conda install -c bioconda blast
Usage
1. Initialize reference database
After finish installation, you should first initialize the reference database using following command
ResBlaster -init
Usage: ResBlaster -i <genome assemble directory> -db <reference database> -o <output_directory> -minid 90 -mincov 60 -t 4
optional arguments:
-h, --help show this help message and exit
-i I <input_path>: the PATH to the directory of assembled genome files
-o O <output_directory>: output PATH
-db DB <database>: resfinder or others, You colud check database list using -list parameter
-minid MINID <minimum threshold of identity>, default=90
-mincov MINCOV <minimum threshold of coverage>, default=60
-list <show database list>
-init <initialize the reference database>
-t T <number of threads>: default=8
-store_arg_seq save the nucleotide and amino acid sequence of find genes on genome
-v, --version Display version
2. Making your own database
Let's say you want to make your own database called owndb
. All you need is a FASTA file of nucleotide sequences, say owndb.fsa
(note: the fasta file must end with .fsa). Ideally the sequence IDs would have the format >GENE___ID___ACC___CATEGORY
where GENE
is the name of GENE
, ID
is the allele ID
of GENE
, ACC
is an accession number of the sequence source, CATEGORY
is the CATEGORY of this GENE belongs to
.
**Your final **owndb.fsa
should like this:
>blaOXA-62___1___AY423074___Beta-lactam
ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCG
GTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAA
GCCGCGTTGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGC
GTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCC
GCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACCTACAAGATATTCAACAGCCTGCTG
GCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCG
CGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGC
CTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTG
AACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGAC
GACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGC
ACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCC
ACGCCGGACTATGTGCTTCACGGCAAGACGGGTTGGTTCGTCGACAAGAAGCCCGATATC
GGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATC
GACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAG
GACCTGAAGCTGATCTGA
**Run following command will add **owndb.fsa
to blast database
% ResBlaster -updatedb owndb.fsa
3. Features under development
Following database are currently under development and will be available soon:
Database | Description |
---|---|
vfdb_core | The core dataset of vfdb |
vfdb_full | The full database of vfdb |
ncbi | Bacterial Antimicrobial Resistance Reference Gene Database from NCBI |
resfinder | ARGs from ResFinder |
ssuis_sero | The serotype database for Streptococcus suis |
hps | The serotype database for Haemophilus parasuis |
lmo | Listeria monocytogenes relevant genes from Pasteur Institute |
ESBL | ESBL genes |
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for ResBlaster-0.4.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 28747b55f724865647dca0df3451035ec55be590a0694ff13add4cc26724ead3 |
|
MD5 | 3955f6ff57326079c79efd9d35c848a8 |
|
BLAKE2b-256 | fe74f347e0671b9dbed93de9a1a96bc5169a59267ac56ba1a4d076eef2015ca1 |