PHASTEST_API

Utility Script for the automation of PHASTEST API Submission and Retrieval. Based on https://phastest.ca/

Reference

Wishart DS, Han S, Saha S, et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023;51(W1):W443-W450. doi:10.1093/nar/gkad382

Prerequisites

OS

Unix/macOS

(Tested on Ubuntu 20.04 and macOS Ventura 13.4)

Programs

jq command

To install jq:

Ubuntu: sudo apt-get install jq

Homebrew: brew install jq

Installation

1. Download phastest_api.sh
2. run "chmod +x phastest_api.sh" to enable execution of the code

Usage

Input path must include genome contig files in the format of ".fna" Output folder will contain a collection of zipped files, each with the prophage summaries.

Default input file is working directory, change it using the --inputDir flag

bash phastest_api.sh [-h|--help] <[--submitjob][--getresults]> [--outDir DIR][--inputDir DIR][--cleanup]

Example:

bash phastest_api.sh --submitjob --inputDir ./00.fnafiles

bash phastest_api.sh --getresults --outDir ./01.phastest_results

bash phastest_api.sh --getresults --outDir ./01.phastest_results --cleanup

Modes:

--submitjob - Parses the genome contig files into the phastest API. Only accepts .fna fasta files and the script will automatically detect if it is a multi-fasta file.

--getresults - Gets the results of job submissions based on json file inputs. (Very important) Please run this after running submit job and allow time for Phastest to run your samples.

Note: Speed in which your samples are ready depends on PHASTEST servers and queue times. This script only automates the file upload and data retrieval.