# 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](https://github.com/tseemann/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](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)
### 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|
Raw data
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"description": "# cvmmlst\n\n\n```\n __ __\n ______ ______ ___ ____ ___ / /____/ /_\n / ___/ | / / __ `__ \\/ __ `__ \\/ / ___/ __/\n/ /__ | |/ / / / / / / / / / / / (__ ) /_\n\\___/ |___/_/ /_/ /_/_/ /_/ /_/_/____/\\__/\n\n\n```\n\ncvmmlst 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](https://github.com/tseemann/mlst) tool.\n\n\n## Installation\n### Using pip\npip3 install cvmmlst\n\n### Using conda\ncomming soon...\n\n## Dependency\n- BLAST+ >2.7.0\n\n**you should add BLAST in your PATH**\n\n\n## Blast installation\n### Windows\n\n\nFollowing this tutorial:\n[Add blast into your windows PATH](http://82.157.185.121:22300/shares/BevQrP0j8EXn76p7CwfheA)\n\n### Linux/Mac\nThe easyest way to install blast is:\n\n```\nconda install -c bioconda blast\n```\n\n\n\n## Usage\n\n### Initialize reference database\n\nAfter finish installation, you should first initialize the reference database using following command\n```\ncvmmlst -init\n```\n\n\n\n```\nusage: cvmmlst -i <genome assemble directory> -o <output_directory>\n\nAuthor: Qingpo Cui(SZQ Lab, China Agricultural University)\n\noptional arguments:\n -h, --help show this help message and exit\n -i I <input_path>: the PATH to the directory of assembled genome files. Could not use with -f\n -f F <input_file>: the PATH of assembled genome file. Could not use with -i\n -o O <output_directory>: output PATH\n -minid MINID <minimum threshold of identity>, default=90\n -mincov MINCOV <minimum threshold of coverage>, default=60\n -init <initialize the reference database>\n -t T <number of threads>: default=8\n -v, --version Display version\n```\n\n### Output\n\nyou will get a text file and a summray file in csv format in the output directory.\n\nThe text file like\n|dat | bglA | cat |ldh |abcZ | dapE | lhkA | ST | Scheme | FILE|\n|---|---|---|---|---|---|---|---|---|---|\n|3 |1 |4| 39 | 12 | 14 | 4 |87 | listeria_2 | 665|\n\nThe content in csv summary file like\n|dat | bglA | cat |ldh |abcZ | dapE | lhkA | ST | Scheme | FILE|\n|---|---|---|---|---|---|---|---|---|---|\n|3 |1 |4| 39 | 12 | 14 | 4 |87 | listeria_2 | sample01|\n|2 |4 |4 |1 |4 |3 |5 |3 |listeria_2 | sample02|\n|6 |6| 8 |37 | 7 |8 |1 |121| listeria_2 | sample03|\n|3 |1 |4| 39 | 12 | 14 | 4 |87 | listeria_2 | sample04|\n|2 |4 |4 |1 |4 |3 |5 |3 |listeria_2 | sample05|\n|6 |6| 8 |37 | 7 |8 |1 |121| listeria_2 | sample06|\n\n\n",
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