Metadata-Version: 2.1
Name: ResBlaster
Version: 0.4.0
Summary: find antimcirobial resistance genes on genomes
Home-page: https://github.com/hbucqp/ResBlaster
Author: Qingpo Cui
Author-email: cqp@cau.edu.cn
License: MIT Licence
Keywords: pip,wgs,blastn,amr
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/markdown
Requires-Dist: Bio
Requires-Dist: pandas
Requires-Dist: setuptools
Requires-Dist: cvmblaster

# ResBlaster

![PYPI](https://img.shields.io/pypi/v/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](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)

### 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                                                           |



