Metadata-Version: 1.0
Name: operondemmo
Version: 0.0.5
Summary: an independent demo of KNOWN operon predict method
Home-page: https://github.com/GodInLove/operondemmo
Author: yaodongliu
Author-email: yd.liu.scu@gmail.com
License: GPLv3
Description-Content-Type: UNKNOWN
Description: operondemmo: an independent demo of KNOWN operon predict method
        ==============================================================================
        |PyPI version| |Docs| |License|
        
        .. contents:: :local:
        
        Library
        --------------------------------------------------------------------------------
        - Python3.6
        - Numpy
        - Pandas
        - Linux(Fedora)
        
        Install
        --------------------------------------------------------------------------------
        
        PyPI
        ^^^^^^^^^^^^^^^^^^^^
        
        .. code-block:: console
        
            $ pip3 install operondemmo --user
        
        
        or `download operondemmo <https://pypi.python.org/pypi/operondemmo/>`_ and install:
        
        .. code-block:: console
        
            $ pip3 install operondemmo-*.tar.gz --user
        
        
        To upgrade to latest version:
        
        .. code-block:: console
        
            $ pip3 install --upgrade operondemmo --user
        
        
        GitHub
        ^^^^^^^^^^^^^^^^^^^^
        
        .. code-block:: console
        
            $ git clone https://github.com/GodInLove/operondemmo.git
            $ cd operondemmo
            $ python3 setup.py install
        
        
        or `download <https://github.com/GodInLove/operondemmo/releases/>`_ and install:
        
        .. code-block:: console
        
            $ pip install operondemmo-*.tar.gz
        
        
        Usage
        --------------------------------------------------------------------------------
        
        Quick start
        ^^^^^^^^^^^^^^^^^^^^
        
        .. code-block:: console
        
            $ git clone https://github.com/GodInLove/operondemmo.git
            $ cd operondemmo/test/count && tar -zxf count.tar.gz
            $ rm -f count.tar.gz
            $ cd ..
            $ operondemmo -i count -g gff/eco.gff
        
        
        Outputs: ``test/OUT/operon.txt``
        
        Basic Parameters
        ^^^^^^^^^^^^^^^^^^^^
        -h
            **PRINT_HELP**
            (show this help message and exit)
        -i
            **INPUT_FILES**
            (A directory to store a group of result files through [samtools depth XXX > xxx.txt] command)
        -o
            **OUTPUT_PATH**
            (A directory include output data(operon file).)
        -g
            **GFF_FILE**
            (The gff file of the prokaryote)
        -t
            **THRESHOLD**
            (the threshold in (-1,1))
        
        Advanced Parameters
        ^^^^^^^^^^^^^^^^^^^^
        --person
           Build co-expression matrix with person correlation
        --spearman
           Build co-expression matrix with spearman correlation
        
        
        
        *cite:*
         1. Junier I, Unal E B, Yus E, et al. Insights into the mechanisms of basal coordination of transcription using a genome-reduced bacterium[J]. Cell systems, 2016, 2(6): 391-401.
        
        
        .. |PyPI version| image:: https://img.shields.io/pypi/v/operondemmo.svg?style=flat-square
           :target: https://pypi.python.org/pypi/operondemmo
        .. |Docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat-square
           :target: https://github.com/GodInLove/operondemmo
        .. |License| image:: https://img.shields.io/aur/license/yaourt.svg?maxAge=2592000
           :target: https://github.com/GodInLove/operondemmo/blob/master/LICENSE.txt
Keywords: operon
Platform: UNKNOWN
