python mlst analysis tool
Project description
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> -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
-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 |
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