operondemmo 0.0.7

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::
example_count/
SRR6322033_count.txt
SRR6322035_count.txt
SRR6322037_count.txt
...


or when ``--kallisto``
.. code-block::
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