AMR_Summary
AMR Summary combines the outputs from ResFinder and MOB-recon to yield reports with genes AMR resistance phenotypes, and whether they are present on plasmids.
Installation
AMR_Summary can be installed using conda
Skip this step if you have already installed conda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
bash miniconda.sh -b -p $HOME/miniconda
conda update -q conda
Quickstart
You can now install the AMR_Summary package:
conda install -c olc-bioinformatics amr_summary
If you encounter the following error:
PackageNotFoundError: Packages missing in current channels:
You need to add one or more of the following channels to your conda install:
- conda-forge
- bioconda
- olcbioinformatics
To see which channels you currently have:
conda config --show channels
To install the missing channel(s)
conda config --append channels olcbioinformatics
conda config --append channels conda-forge
conda config --append channels bioconda
Tests
If you encounter issues with the AMR_Summary package, tests are available to ensure that the installation was successful and your credentials are valid.
You will need to clone this repository and run the tests with pytest:
git clone https://github.com/OLC-Bioinformatics/AMR_Summary.git
cd AMR_Summary
python -m pytest tests/ --cov=amr_summary -s -vvv
Running AMR_Summary
Arguments
You can be supply absolute, tilde slash, or relative paths or all path arguments
Required Arguments
- sequence path: name and path of folder containing sequences to process
- database path: name and path of folder containing ResFinder and MOB-recon databases. Note that you do not need to download these databases. The will be downloaded and initialised as part of the script
Optional Arguments
- report path: name and path of folder in which reports are to be created. Default is sequence_path/reports
- debug: print debug-level logs to console
- version: print version of AMR_Summary
Example command
To process sequence files in FASTA format in the folder ~/Analyses/sequences
, use databases in /databases
, and place reports in your current working directory
AMR_Summary -s ~/Analyses/sequences -d /databases -r .
Usage
usage: AMR_Summary [-h] -s -d [-r] [--debug] [-v]
AMR Summary: a pipeline to identify AMR resistance genes located on plasmids
by combining ResFinder and MOB-recon
optional arguments:
-h, --help show this help message and exit
-s , --sequence_path
Path of folder containing sequence files in FASTA
format to process
-d , --database_path
Path of folder containing ResFinder and MOB-recon
databases. If these databases cannot be located, they
will be downloaded
-r , --report_path Path of folder in which reports are to be created.
Default is sequence_path/reports
--debug Enable debug-level messages to be printed to the
console
-v, --version show program's version number and exit