Metadata-Version: 1.0
Name: operondemmo
Version: 0.0.12
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
        
           $ operondemmo -i input_dir -f fna_file_path -g gff_file_path
        
        
        
        Outputs: ``test/OUT/operon.txt``
        
        Or:
        
        .. code-block:: console
        
           $ operondemmo -i input_dir -f fna_file_path -g gff_file_path -o out_dir -t threshold
        
        
        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).
        -f
            **FNA_FILE:**
            The fna file of the prokaryote genome.
        -p
            **PROCESS_NUM**
            Specify the number of processing threads.
        
        
        **INPUT_DIR:**
        
        
        .. code-block:: console
        
           example_input/
              c1/
                 SRR6322033_1.fastq.gz
                 SRR6322033_2.fastq.gz
              c2/
                 SRR6322035_1.fastq.gz
                 SRR6322035_2.fastq.gz
              c3/
                 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
        
        
        *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.
         2. Bray N L, Pimentel H, Melsted P, et al. Near-optimal probabilistic RNA-seq quantification[J]. Nature biotechnology, 2016, 34(5): 525.
        
        .. |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: http://lyd.ourblogs.me/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
