cvmmlst 0.3.2

python mlst analysis tool

cvmmlst

                                  __     __
  ______   ______ ___  ____ ___  / /____/ /_
 / ___/ | / / __ `__ \/ __ `__ \/ / ___/ __/
/ /__ | |/ / / / / / / / / / / / (__  ) /_
\___/ |___/_/ /_/ /_/_/ /_/ /_/_/____/\__/

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