Metadata-Version: 1.0
Name: operondemmo
Version: 0.0.11
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:
        
        Dependencies
        --------------------------------------------------------------------------------
        - `Python3.6 <https://www.python.org/>`_
        - `Numpy <http://www.numpy.org>`_
        - `Pandas <https://pandas.pydata.org/>`_
        - Linux(Fedora)
        - `Kallisto <https://pachterlab.github.io/kallisto/>`_
        
        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
        
            $ wget https://github.com/GodInLove/operondemmo/archive/master.zip
            $ unzip operondemmo-master.zip
            $ cd operondemmo-master
            $ 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
        
           $ mkdir test
           $ wget http://lyd.ourblogs.me/operondemmo/test/count.tar.gz
           $ wget http://lyd.ourblogs.me/operondemmo/test/gff/eco.gff
           $ cd tar -zxf count.tar.gz
           $ rm -f count.tar.gz
           $ operondemmo -i count -g eco.gff
        
        
        Outputs: ``test/OUT/operon.txt``
        
        Basic Parameters
        ^^^^^^^^^^^^^^^^^^^^
        -h
            **PRINT_HELP:**
            show this help message and exit
        -i
            **INPUT_DIR:**
            A directory to store a group of files.
        -o
            **OUTPUT_DIR:**
            A directory include output data(operon file).
        -g
            **GFF_FILE:**
            The gff file of the prokaryote
        -t
            **THRESHOLD**
            the threshold in (-1,1)
        
        
        **INPUT_DIR:**
        
        default: [samtools depth] result files
        
        
        .. code-block:: console
        
            example_count/
              SRR6322033_count.txt
              SRR6322035_count.txt
              SRR6322037_count.txt
              ...
        
        
        or when ``--kallisto``
        
        .. code-block:: console
        
           example_input/
              eco.fna
              SRR6322033_1.fastq.gz
              SRR6322033_2.fastq.gz
              SRR6322035_1.fastq.gz
              SRR6322035_2.fastq.gz
              SRR6322037_1.fastq.gz
              SRR6322037_2.fastq.gz
              ...
        
        
        Advanced Parameters
        ^^^^^^^^^^^^^^^^^^^^
        --person
           Build co-expression matrix with person correlation
        --spearman
           Build co-expression matrix with spearman correlation
        --kallisto
           Build expression matrix with kallisto result
        
        
        *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
