Metadata-Version: 2.1
Name: GenomeQAML
Version: 0.0.12
Summary: CFIA OLC Genome Quality Assessment with Machine Learning
Home-page: https://github.com/OLC-LOC-Bioinformatics/GenomeQAML
Author: OLC Bioinformatics
Author-email: adam.koziol@inspection.gc.ca
License: MIT
Description: [![Build status](https://travis-ci.org/OLC-LOC-Bioinformatics/GenomeQAML.svg?master)](https://travis-ci.org/OLC-LOC-Bioinformatics)
        # GenomeQAML: Genome Quality Assessment with Machine Learning
        
        The GenomeQAML is a script that uses a pre-computed ExtraTreesClassifier model in order to 
        classify FASTA-formatted _de novo_ assemblies as bad, good, or very good. It's easy to use,
        and has minimal dependencies.
        
        ## External Dependencies
        
        - [Mash (v2.0 or greater)](https://github.com/marbl/mash)
        - [Prodigal (>=2.6.2)](https://github.com/hyattpd/Prodigal)
        
        Both of these need to be downloaded and included on your $PATH.
        
        ## Installation
        
        All you need to do is install with pip: `pip install genomeqaml`. 
        
        Usage of a virtualenv
        is highly recommended.
        
        ## Usage
        
        GenomeQAML takes a directory containing uncompressed fasta files as input - these will be classified and a
         report written to a CSV-formatted file for your inspection.
        
        To run, type `classify.py -t /path/to/fasta/folder`
        
        This will create a report, by default called `QAMLreport.csv`. You can change the name 
        of the report with the `-r` argument.
        
        ```
        usage: classify.py [-h] -t TEST_FOLDER [-r REPORT_FILE]
        
        optional arguments:
          -h, --help            show this help message and exit
          -t TEST_FOLDER, --test_folder TEST_FOLDER
                                Path to folder containing FASTA files you want to
                                test.
          -r REPORT_FILE, --report_file REPORT_FILE
                                Name of output file. Default is QAMLreport.csv.
        
        ```
        
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Description-Content-Type: text/markdown
