Metadata-Version: 1.1
Name: pyim
Version: 0.2.0
Summary: Tool for identifying transposon insertions from targeted DNA-sequencing data.
Home-page: https://github.com/jrderuiter/pyim
Author: Julian de Ruiter
Author-email: julianderuiter@gmail.com
License: MIT license
Description: ===============================
        PyIM
        ===============================
        
        .. image:: https://img.shields.io/travis/jrderuiter/pyim.svg
                :target: https://travis-ci.org/jrderuiter/pyim
        
        PyIM (Python Insertional Mutagenesis) is a python package for analyzing
        insertional mutagenesis data from targeted sequencing of transposon insertion
        sites. The package provides several command line tools for identifying
        insertions, calling common insertion sites (CISs) and annotating
        insertions/CISs directly from the command line. It also aims to provides
        the basic building blocks for implementing new pipelines, CIS callers, etc.
        
        Documentation
        -------------
        
        PyIM's documentation is available at
        `jrderuiter.github.io/pyim <http://jrderuiter.github.io/pyim/>`_.
        
        
        Requirements
        ------------
        
        PyIM is written for Python 3 and requires Python 3.3 or newer to be installed.
        Depending on the used functionality, PyIM also has the following external
        dependencies:
        
        - cutadapt/bowtie2 (Needed for identifying insertions from sequencing data)
        - cimpl (R package, needed for calling CIS sites using CIMPL)
        
        Installation
        ------------
        
        Using conda
        ~~~~~~~~~~~
        
        The recommended way to install PyIM is using conda, as with conda you can
        install PyIM together with its external dependencies (cutadapt and bowtie2)
        into an isolated environment using a single command:
        
        .. code:: bash
        
            conda create -n pyim -c jrderuiter -c bioconda -c r pyim
        
        Alternatively, PyIM can be installed in an existing environent using:
        
        .. code:: bash
        
            conda install -c jrderuiter -c bioconda -c r pyim
        
        Conda packages are available for both OSX and Linux (64-bit).
        
        Using pip
        ~~~~~~~~~
        
        PyIM can be installed from Github using pip as follows:
        
        .. code:: bash
        
            pip install git+git://github.com/jrderuiter/pyim.git#egg=pyim
        
        Note that in this case, external dependencies must be installed manually.
        
        Unfortunately, PyIM is not yet available on PyPI, though this may
        change when the package is further developed.
        
        License
        -------
        
        This software is released under the MIT license.
        
        
        =======
        History
        =======
        
        0.2.0 (2017-05-10)
        ------------------
        
        * Refactored pipeline structure.
        * Added ShearSplink and Nextera pipelines.
        
        0.1.0 (2016-09-01)
        ------------------
        
        * Initial release.
        
Keywords: pyim
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
