Metadata-Version: 2.1
Name: frast
Version: 0.1.0
Summary: 
Author: Jackson Greene
Author-email: jackson.greene@student.curtin.edu.com
Requires-Python: >=3.8,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Dist: requests[all] (>=2.27.1,<3.0.0)
Requires-Dist: typer[all] (>=0.4.1,<0.5.0)
Description-Content-Type: text/markdown

# FRAST

The command line version of FRAST
Generates an output json file with data including MAFFT output, mutions for each sequence and related papers

# frast --help

Usage: frast [OPTIONS]

Options:
--m TEXT mode of archetype selection: automatic, reference, or
custom [default: automatic]
--a TEXT relative path to the custom archetype fasta file
--i TEXT relative path to the test sequences fasta file
[required]
--o TEXT output file prefix (extension will be .json automatically) [default:
output_file]
--help Show this message and exit.

# example commands

(automatically selecting archetype using input sequences)
frast --m automatic --i test_input.fasta --o output_file

(using one of the reference archetypes by name)
frast --m reference --a CytB --i test_input.fasta --o output_file

(using a custom archetype by fasta file)
frast --m custom --a test_archetype.fasta --i test_input.fasta --o output_file

