PlasmidHostMahalanobisMatcher is a software for predicting the possible host for given plasmids based on multiple features.

• This software requires Python 3, install Python3 or Anaconda3

• The packages used in this software is included in requirements.txt
• If you are using pip, run pip install -r requirements.txt in the console
• If you are using conda, run conda install --file requirements.txt in the console

• Download the repository and unzip or clone the repository

  git clone https://github.com/dorasir/PlasmidHostMahalanobisMatcher
  

• For MacOS, run the following command to setup

  MACOSX_DEPLOYMENT_TARGET=10.9 CC=g++ python setup.py install --install-platlib=src
  

• For Linux, run the following command to setup

  CC=g++ python setup.py install --install-platlib=src
  

Our constructed host bacteria database is available for this software, the database can be downloaded at GoogleDrive. The content of the downloaded archive should then be extracted to data folder of the software directory.

python PlasmidHostMahalanobisMatcher.py [-h] -q QUERY_PLASMID_DIR -o OUTPUT [-t NUM_THREADS] [-n topN] [-i INTERMEDIATE_DIR]

-h, --help            show this help message and exit
-q QUERY_PLASMID_DIR  Directory containing query plasmid genomes with .fasta or .fa suffix
-o OUTPUT             Output file
-t NUM_THREADS        Number of threads to use. Default = 1
-n topN               Number of top predictions written to the output files. All predictions will be output if there is a tie in score. Default = 1
-i INTERMEDIATE_DIR   Directory storing intermediate result. Default = ./intermediate_res

To predict the host of plasmids of interest, put the genome of the plasmids into a dedicated folder, for example, plasmids. The prediction can then be made by running

python PlasmidHostMahalanobisMatcher.py -q plasmids

By default the prediction result will be stored in output.txt under the software folder.