Metadata-Version: 1.1
Name: changeo
Version: 0.3.1
Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Home-page: http://clip.med.yale.edu/changeo
Author: Namita Gupta
Author-email: namita.gupta@yale.edu
License: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
Description: Version 0.3.1: December 18, 2015
        ================================
        
        Change-O is a collection of tools for analyzing immunoglobulin
        sequences. Dramatic improvements in high-throughput sequencing
        technologies now enable large-scale characterization of immunoglobulin
        (Ig) repertoires, defined as the collection of trans-membrane
        antigen-receptor proteins located on the surface of T and B lymphocytes.
        Change-O is a suite of utilities to handle advanced analysis of Ig
        sequences following germline segment assignment. Change-O handles output
        from IMGT/HighV-QUEST and IgBLAST. It includes features for creating a
        personalized genotype, identifying sequences that are from a single B
        cell clone and inferring its lineage tree, analyzing amino acid
        properties, calculating diversity, generating a model of somatic
        hypermutation, and quantifying selection pressure. Record sorting,
        grouping, and sampling operations are also included.
        
        Requirements
        ------------
        
        -  `Python 3.4.0 <http://python.org>`__
        -  `setuptools 2.0 <http://bitbucket.org/pypa/setuptools>`__
        -  `NumPy 1.8 <http://numpy.org>`__
        -  `SciPy 0.14 <http://scipy.org>`__
        -  `pandas 0.15 <http://pandas.pydata.org>`__
        -  `Biopython 1.65 <http://biopython.org>`__
        -  `presto 0.5 <http://clip.med.yale.edu/presto>`__
        -  `MUSCLE v3.8 <http://www.drive5.com/muscle>`__
        
        Installation - Linux
        --------------------
        
        1. The simplest way to install all Python dependencies is to install the
           full SciPy stack using the
           `instructions <http://scipy.org/install.html>`__, then install
           Biopython according to its
           `instructions <http://biopython.org/DIST/docs/install/Installation.html>`__.
        
        2. Install pRESTO 0.5.0 or greater from
           `here <http://clip.med.yale.edu/presto>`__.
        
        3. | Extract the Change-O bundle and run:
           |  ``> python3 setup.py install --user``
        
        Installation - Windows
        ----------------------
        
        1. Install Python 3.4.0+ from `Python <http://python.org/downloads>`__,
           selecting both the options 'pip' and 'Add python.exe to Path'.
        
        2. Install NumPy, SciPy, pandas and Biopython using the packages
           available from the `Unofficial Windows
           binary <http://www.lfd.uci.edu/~gohlke/pythonlibs>`__ collection.
        
        3. | Unzip the Change-O bundle, open a Command Prompt, change
             directories to the Change-O folder, and run:
           |  ``> python setup.py install``.
        
        4. For a default installation of Python 3.4, the Change-O scripts will
           be installed into ``C:\Python34\Scripts`` and should be directly
           executable from the Command Prompt. If this is not the case, then
           follow step 5 below.
        
        5. Add both the ``C:\Python34`` and ``C:\Python34\Scripts`` directories
           to your ``%Path%``. On Windows 7 the ``%Path%`` setting is located
           under Control Panel -> System and Security -> System -> Advanced
           System Settings -> Environment variables -> System variables -> Path.
        
        Installation - Mac OS X
        -----------------------
        
        1. Install Xcode 3.2.6 Available from the Apple store or `developer
           downloads <http://developer.apple.com/downloads>`__. If you have a
           newer version (eg, Xcode 4.6.3) that will work also, but Xcode 3 is
           free of charge. If Xcode fails to install with an "Unknown Error",
           change the date on your system to some time in 2011, install Xcode,
           and then change the date back to the proper setting.
        
        2. Install XQuartz 2.7.5 Available from the `XQuartz
           project <http://xquartz.macosforge.org/landing>`__.
        
        3. Install Homebrew Follow the installation and post-installation
           `instructions <http://brew.sh>`__.
        
        4. | Open a terminal and install gfortran (required for SciPy) using
             Homebrew (this can take an hour to install):
           |  ``> brew install gfortran``
           |  If the above fails run this instead:
           |  ``> brew install --env=std gfortran``
        
        5. | Install Python 3.4.0+ and set the path to the python3 executable:
           |  ``> brew install python3``
           |  ``> echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profile``
           |  Exit and reopen the terminal application so the PATH setting takes
             effect
        
        6. | Install NumPy, SciPy, pandas and Biopyton using the Python package
             manager:
           |  ``> pip3 install numpy scipy pandas biopython``
        
        7. | Extract the Change-O bundle, open a terminal window, change
             directories to the Change-O folder, and run:
           |  ``> python3 setup.py install``
        
Keywords: bioinformatics immunoglobulin lymphocyte sequencing
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
