New upstream version 2.2.1

# TRANSIT 2.1.2

# TRANSIT 2.2.1

[![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest) 

**Version 2.2.0 changes (June, 2018)**

- Added analysis method for Genetic Interactions.

- Added Mann-Whitney U-test for comparative analysis.

- Made TRANSIT compatible with wxPython 4.0 (Phoenix).

- Datasets now automatically selected when they are added to TRANSIT.

- TRANSIT window now starts maximized.

- Updated documentation.

- Fixed bug with plots of finished results files.

- Fixed bug in packaging of TPP, causing problem with console mode in new setuptools.

- Other misc. bugs fixes

**Version 2.1.2 changes (May, 2018)**

- Improved resampling on comparisons with unbalanced number of replicates.

TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.

## Features

TRANSIT offers a variety of features including:

-   More than **8 analysis methods**, including methods for determining **conditional essentiality** as well as **genetic interactions**.

-   Ability to analyze datasets from libraries constructed using  **himar1 or tn5 transposons**.

-   **TrackView** to help visualize read-counts accross the genome.

-   Can **export datasets** into a variety of formats, including **IGV**.

-   Includes a **variety of normalization methods**.

-   **Quality Control** diagnostics, to idenfity poor quality datasets.

-   Ability to install as a **python package**, to import and use in your own personal scripts.

## Mailing List

version: 2.1.2-1-gccf8-mod

version: 2.2.0-6-g2c24-mod

    # your project is installed. For an analysis of "install_requires" vs pip's

    # requirements files see:

    # https://packaging.python.org/en/latest/requirements.html

    install_requires=['setuptools', 'numpy', 'scipy', 'pillow', 'matplotlib'],

    install_requires=['setuptools', 'numpy', 'scipy', 'pillow', 'matplotlib', 'wxpython'],

    #dependency_links = [

    #	"git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"

    # pip to create the appropriate form of executable for the target platform.

    entry_points={

        'console_scripts': [

            'transit=pytransit.__main__:main',

            'tpp=pytpp.__main__:main',

            'transit=pytransit.__main__:run_main',

            'tpp=pytpp.__main__:run_main',

        ],

    },

)

from tpp_gui import *

def main(arguments=[]):

def run_main():

    (args, kwargs) = cleanargs(sys.argv[1:])

    main(*args, **kwargs)

    vars = Globals()

def main(*args, **kwargs):

    if len(arguments)==0 and hasWx:        

    vars = Globals()

    # Check for arguements

    if not args and not kwargs and hasWx:        

        app = wx.App(False)

        form = MyForm(vars)

        form.update_dataset_list()

        else:

            pass

    elif len(arguments) <= 1 and not hasWx:

    elif not args and not kwargs and not hasWx:

        print "Please install wxPython to run in GUI Mode."

        print "To run in Console Mode please follow these instructions:"

        print ""

        show_help()

    else:

        (args, kwargs) = cleanargs(arguments)

        # Show help if needed

        if "help" in kwargs or "-help" in kwargs:

if __name__ == "__main__":

    main(sys.argv[1:])

    run_main()

__all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]

__version__ = "v2.1.2"

__version__ = "v2.2.1"

prefix = "[TRANSIT]"