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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: The speed at which your samples are ready depends on PHASTEST servers and queue times. This script only automates the file upload and data retrieval.