python mlst analysis tool


Keywords
wgs, pubmlst, mlst
License
MIT
Install
pip install cvmmlst==0.3.2

Documentation

cvmmlst

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cvmmlst is a bacteria mlst analysis tool that could run on Windows, Linux and MAC os. Some of the code ideas in cvmmlst draw on Torsten Seemanns excellent mlst tool.

Installation

Using pip

pip3 install cvmmlst

Using conda

comming soon...

Dependency

  • BLAST+ >2.7.0

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

Initialize reference database

After finish installation, you should first initialize the reference database using following command

cvmmlst -init
usage: cvmmlst -i <genome assemble directory> -o <output_directory>

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

optional arguments:
  -h, --help      show this help message and exit
  -i I            <input_path>: the PATH to the directory of assembled genome files. Could not use with -f
  -f F            <input_file>: the PATH of assembled genome file. Could not use with -i
  -o O            <output_directory>: output PATH
  -minid MINID    <minimum threshold of identity>, default=90
  -mincov MINCOV  <minimum threshold of coverage>, default=60
  -init           <initialize the reference database>
  -t T            <number of threads>: default=8
  -v, --version   Display version

Output

you will get a text file and a summray file in csv format in the output directory.

The text file like

dat bglA cat ldh abcZ dapE lhkA ST Scheme FILE
3 1 4 39 12 14 4 87 listeria_2 665

The content in csv summary file like

dat bglA cat ldh abcZ dapE lhkA ST Scheme FILE
3 1 4 39 12 14 4 87 listeria_2 sample01
2 4 4 1 4 3 5 3 listeria_2 sample02
6 6 8 37 7 8 1 121 listeria_2 sample03
3 1 4 39 12 14 4 87 listeria_2 sample04
2 4 4 1 4 3 5 3 listeria_2 sample05
6 6 8 37 7 8 1 121 listeria_2 sample06