Metadata-Version: 2.1
Name: GMGC-mapper
Version: 0.2.0
Summary: Map genes and genome to the Global Microbial Gene Catalog (GMGC)
Home-page: https://github.com/BigDataBiology/GMGC-mapper
Author: Shaojun Pan
Author-email: shaojun1997777@gmail.com
License: MIT
Description: # GMGC-mapper
        
        [![Install with conda](https://anaconda.org/bioconda/gmgc-mapper/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)
        [![PyPI version](https://badge.fury.io/py/GMGC-mapper.svg)](https://badge.fury.io/py/GMGC-mapper)
        ![gmgc_mapper_test](https://github.com/BigDataBiology/GMGC-Finder/workflows/gmgc_mapper_test/badge.svg)
        [![Number of downloads](https://anaconda.org/bioconda/gmgc-mapper/badges/downloads.svg)](https://anaconda.org/bioconda/gmgc-mapper)
        [![License: MIT](https://anaconda.org/bioconda/gmgc-mapper/badges/license.svg)](https://anaconda.org/bioconda/gmgc-mapper)
        
        
        Command line tool to query the Global Microbial Gene Catalog (GMGC).
        
        ## Install
        
        GMGC-mapper runs on Python 3.6-3.8 and requires
        [prodigal](https://github.com/hyattpd/Prodigal) to be available for genome
        mode.
        
        ### Conda install
        
        The easiest way to install GMGC-mapper is through bioconda, which will ensure
        all dependencies (including `prodigal`) are installed automatically:
        
        ```bash
        conda install -c bioconda gmgc-mapper
        ```
        
        ### pip install
        
        Alternatively, `GMGC-mapper` is available from PyPI, so can be installed
        through pip:
        
        ```bash
        pip install GMGC-mapper
        ```
        
        Note that this does not install `prodigal` (which is necessary for the
        genome-based workflow).
        
        ### Install from source
        
        Finally, especially if you are retrieving the cutting edge version from Github,
        you can install with the standard
        
        ```bash
        python setup.py install
        ```
        
        
        ## Examples
        
        1. Input is a genome sequence.
        
        ```bash
        gmgc-mapper -i input.fasta -o output
        ```
        
        2. Input is DNA/protein gene sequences
        
        ```bash
        gmgc-mapper --nt-genes genes.fna --aa-genes genes.faa -o output
        ```
        
        The nucleotide input is optional (but should be used if available so that the
        quality of the hits can be refined):
        
        ```bash
        gmgc-mapper --aa-genes genes.faa -o output
        ```
        
        If yout input is a metagenome, you can use
        [NGLess](https://github.com/ngless-toolkit/ngless) for assembly and gene
        prediction. For more details, [read the
        docs](https://gmgc-mapper.readthedocs.io/en/latest/usage/).
        
        ## Output
        
        The output folder will contain
        
        1. Outputs of gene prediction (prodigal).
        2. Complete data table, listing all the hits in GMGC, per gene.
        3. Complete table, listing all the genome bins (MAGs) that are found in the results.
        4. Human readable summary.
        
        For more details, [read the
        docs](https://gmgc-mapper.readthedocs.io/en/latest/output/). A description of
        the outputs is also written to output folder for convenience.
        
        ## Parameters
        
        * `-i/--input`: path to the input genome file(.fasta/.gz/.bz2).
        
        * `-o/--output`: Output directory (will be created if non-existent).
        
        * `--nt-genes`: path to the input DNA gene file(.fasta/.gz/.bz2).
        
        * `--aa-genes`: path to the input Protein gene file(.fasta/.gz/.bz2).
        
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
