New upstream version 2.3.3

# Change log

All notable changes to this project will be documented in this file.

## Version 2.3.3 2018-12-06

- TRANSIT:	

  - Minor bug fixes related to flags in HMM

## Version 2.3.2 2018-11-09

- TRANSIT:	

  - Minor bug fixes related to changing parameters in TPP GUI

# TRANSIT 2.3.2

# TRANSIT 2.3.3

[![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) 

Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab.

Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab at Texas A&M University.

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.

TRANSIT is a tool for processing and statistical 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.

TRANSIT Home page: http://saclab.tamu.edu/essentiality/transit/index.html

TRANSIT Documentation: https://transit.readthedocs.io/en/latest/transit_overview.html

[Changelog](https://github.com/mad-lab/transit/blob/master/CHANGELOG.md)

For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("src/pytransit/doc" folder) or visit the following web page:

http://saclab.tamu.edu/essentiality/transit/transit.html

https://transit.readthedocs.io/en/latest/

## Datasets

"""

# Always prefer setuptools over distutils

from setuptools import setup, find_packages

from setuptools import setup, find_packages, Command

# To use a consistent encoding

from codecs import open

from os import path

from shutil import rmtree

import os

here = path.abspath(path.dirname(__file__))

import sys

sys.path.insert(1, "src/")

import pytransit

version =  pytransit.__version__[1:] #"2.0.3"

version =  pytransit.__version__[1:]

class UploadCommand(Command):

    """Support setup.py upload."""

    description = 'Build and publish the package.'

    user_options = []

    @staticmethod

    def status(s):

        """Prints things in bold."""

        print('\033[1m{0}\033[0m'.format(s))

    def initialize_options(self):

        pass

    def finalize_options(self):

        pass

    def yes_or_no(self, question):

        while True:

            reply = str(raw_input(question +' (y/n): ')).lower().strip()

            if reply == 'y':

                return True

            return False

    def run(self):

        try:

            self.status('Removing previous builds...')

            rmtree(os.path.join(here, 'dist'))

        except OSError:

            pass

        if not self.yes_or_no("Have you done the following? \n" +

                    "- Updated README/Documentation?\n"

                    "- Have you updated CHANGELOG?\n"

                    "- Have you updated Transit Essentiality page?\n"

                    "- Is version v{0} correct".format(version)):

            self.status("Exiting...")

            sys.exit()

        self.status('Building Source and Wheel (universal) distribution...')

        os.system('{0} setup.py sdist bdist_wheel'.format(sys.executable))

        if self.yes_or_no("Add tag and push to public github? tag:v{0}".format(version)):

            self.status('Adding and pushing git tags to origin and public...')

            os.system('git tag v{0}'.format(version))

            os.system('git push origin --tags')

            os.system('git push https://github.com/mad-lab/transit')

            os.system('git push https://github.com/mad-lab/transit --tags')

        else:

            self.status("Exiting...")

            sys.exit()

        if self.yes_or_no("Proceed with publish to PyPI? version: v{0}, tag:v{0}".format(version)):

            self.status('Uploading the package to PyPI via Twine...')

            os.system('twine upload dist/*')

        else:

            self.status("Exiting...")

            sys.exit()

        sys.exit()

setup(

    name='tnseq-transit',

            'tpp=pytpp.__main__:run_main',

        ],

    },

    cmdclass={

        'upload': UploadCommand,

    },

)

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

__version__ = "v2.3.2"

__version__ = "v2.3.3"

prefix = "[TRANSIT]"

        output_file = open(outpath, "w")

        replicates = kwargs.get("r", "Mean")

        normalization = kwargs.get("r", "TTR")

        normalization = kwargs.get("n", "TTR")

        LOESS = kwargs.get("l", False)

        ignoreCodon = True

        NTerminus = float(kwargs.get("iN", 0.0))

        Optional Arguments:

            -r <string>     :=  How to handle replicates. Sum, Mean. Default: -r Mean

            -n <string>     :=  Normalization method. Default: -n TTR

            -l              :=  Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.

            -iN <float>     :=  Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0

            -iC <float>     :=  Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0