Metadata-Version: 2.1
Name: MirMachine
Version: 0.2.11
Summary: MirMachine
Home-page: https://github.com/sinanugur/MirMachine
Author: Sinan U. Umu
Author-email: sinanugur@gmail.com
License: UNKNOWN
Description: # MirMachine
        
        [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)  [![PyPI version](https://badge.fury.io/py/MirMachine.svg)](https://badge.fury.io/py/MirMachine)  [![Anaconda-Server Badge](https://anaconda.org/bioconda/mirmachine/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)  [![Anaconda-Server Badge](https://anaconda.org/bioconda/mirmachine/badges/downloads.svg)](https://anaconda.org/bioconda/mirmachine)  
        A command line to tool detect miRNA homologs in genome sequences.
        
        
        Installation
        ------------
        To install this package with conda run:
        
        ```
        conda install -c bioconda mirmachine
        ```
        
        
        Alternative method:
        ```
        git clone https://github.com/sinanugur/MirMachine.git
        cd MirMachine
        pip install .
        ```
        
        Check if the installation works by calling the main script.
        ```
        MirMachine.py --help
        ```
        
        Quick start example
        -------------------
        Create a new directory and run MirMachine there after the installation. MirMachine will create the required directories while running.
        ```
        MirMachine.py -n Caenorhabditis -s Caenorhabditis_elegans --genome sample/genomes/ce11.fa -m proto --cpu 20
        ```
        
        Options and Arguments
        ---------------------
        ```
        Usage:
            MirMachine.py --node <text> --species <text> --genome <text> [--model <text>] [--cpu <integer>] [--add-all-nodes|--single-node-only] [--dry]
            MirMachine.py --species <text> --genome <text> --family <text> [--model <text>] [--dry]
            MirMachine.py --print-all-nodes
            MirMachine.py (-h | --help)
            MirMachine.py --version
        
        Arguments:
            -n <text>, --node <text>              Node name. (e.g. Caenorhabditis)
            -s <text>, --species <text>           Species name. (e.g. Caenorhabditis_elegans)
            -g <text>, --genome <text>            Genome fasta file location (e.g. data/genome/example.fasta)
            -m <text>, --model <text>             Model type: deutero, proto, combined [default: proto]
            -f <text>, --family <text>            Run only a single miRNA family.
            -c <integer>, --cpu <integer>         CPUs. [default: 2]
        
        Options:
            -a --add-all-nodes                 Move on the tree both ways.
            -o --single-node-only              Run only the given node.
            -d --dry                           Dry run.
            -p --print-all-nodes               Print all available nodes and exit.
            -h --help                          Show this screen.
            --version                          Show version.
        ```
        
        Output
        ------
        The `MirMachine` main executable will generate GFF annotations (filtered and unfiltered) and some other files.
        You will see `results/predictions/` directory which contains:
        
        `gff/` __All predicted miRNA families.__  
        `filtered_gff/` __High confidence miRNA family predictions after bitscore filtering.__  
        `fasta/` __Both high and low confidence predictions in FASTA format.__  
        
        
        
        
Keywords: RNA miRNA detection prediction
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Provides-Extra: dev
