bacphlip 0.9

A Random Forest classifier to predict bacteriophage lifestyle

BACPHLIP - a bacteriophage lifestyle prediction tool

Adam J. Hockenberry and Claus O. Wilke

Reference:

(eventual manuscript reference here)

Installation

You can install BACPHLIP with pip (NOTE: NOT YET WORKING):

pip install bacphlip

Alternatively, users can pull/download the github repository, navigate to the directory where BACPHLIP was downloaded and run:

pip install .

BACPHLIP has several required dependencies outside of the standard library: biopython, pandas, joblib, and scikit-learn.

Additionally, users are required to install the HMMER3 software suite (in addition to the installation routes listed on the HMMER3 website we note that this tool can also be installed via conda). By default, BACPHLIP assumes that HMMER3 is installed in the system path, but local paths may be provided as run-time flags (see below).

Examples

The most straightforwad usage of BACPHLIP is as a command line tool. Assuming that /valid/path/to/a/genome.fasta exists, you can call BACPHLIP with the command:

python -m bacphlip -i /valid/path/to/a/genome.fasta

This command should create 4 seperate files in the path of the target genome.fasta with genome.fasta.bacphlip containing the final model predictions (tab-separated format) in terms of probability of the input phage being either "Virulent" or "Temperate" (the other files append .6frame, .hmmsearch, and .hmmsearch.tsv to the genome file). Attempting to run this command a second time, assuming the first worked, should create an error since the output files already exist. This behavior can be altered with a flag to force overwrite the files:

python -m bacphlip -i /valid/path/to/a/genome.fasta -f 

Finally, a path to a local HMMER3 install (specifically, the hmmsearch tool) can be specified in the command line:

python -m bacphlip -i /valid/path/to/a/genome.fasta --local_hmmsearch /valid/path/to/hmmsearch

Next steps

We have several planned next steps, including:

1. adding a tutorial for library usage as a jupyter notebook in a forthcoming examples folder.
2. adding the ability to run the pipeline in a "quiet" mode
3. adding a flag for batch input of sequences.

Misc

The software is provided to you under the MIT license (see file LICENSE.txt). The most up-to-date version of this software is available at https://github.com/adamhockenberry/bacphlip.

The development of BACPHLIP is provided in a separate repository for transparency. See bacphlip-model-dev.

Contributing

Pull requests addressing errors or adding new functionalities are welcome on GitHub. However, to be accepted, contributions must pass the pytest unit tests.