Metadata-Version: 1.1
Name: changeo
Version: 0.3.3
Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Home-page: http://changeo.readthedocs.io
Author: Namita Gupta
Author-email: namita.gupta@yale.edu
License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported
Download-URL: https://bitbucket.org/kleinstein/changeo/downloads
Description: Change-O - Repertoire clonal assignment toolkit
        ================================================================================
        
        Change-O is a collection of tools for processing the output of V(D)J alignment
        tools, assigning clonal clusters to immunoglobulin sequences, and reconstructing
        germline 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 facilitate advanced 
        analysis of Ig and TCR sequences following germline segment assignment. Change-O 
        handles output from IMGT/HighV-QUEST and IgBLAST, and provides a wide variety of
        clustering methods for assigning clonal groups to Ig sequences. Record sorting, 
        grouping, and various database manipulation operations are also included.
        
        
        
        Installation
        ================================================================================
        
        The simplest way to install the latest stable release of Change-O is via pip::
        
            > pip3 install changeo --user
        
        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://presto.readthedocs.io>`__
        
        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 <http://presto.readthedocs.io>`__ or greater.
        
        3. Download the Change-O bundle and run::
        
           > pip3 install changeo-x.y.z.tar.gz --user
        
        Mac OS X
        --------------------------------------------------------------------------------
        
        1. Install Xcode. Available from the Apple store or
           `developer downloads <http://developer.apple.com/downloads>`__.
        
        2. Older versions Mac OS X will require you to install XQuartz 2.7.5. Available
           from the `XQuartz project <http://xquartz.macosforge.org/landing>`__.
        
        3. Install Homebrew following the installation and post-installation
           `instructions <http://brew.sh>`__.
        
        4. Install Python 3.4.0+ and set the path to the python3 executable::
        
           > brew install python3
           > echo 'export PATH=/usr/local/bin:$PATH' >> ~/.profile
        
        5. Exit and reopen the terminal application so the PATH setting takes effect.
        
        6. You may, or may not, need to install gfortran (required for SciPy). Try
           without first, as this can take an hour to install and is not needed on
           newer releases. If you do need gfortran to install SciPy, you can install it
           using Homebrew::
        
           > brew install gfortran
        
           If the above fails run this instead::
        
           > brew install --env=std gfortran
        
        7. Install NumPy, SciPy, pandas and Biopyton using the Python package
           manager::
        
           > pip3 install numpy scipy pandas biopython
        
        8. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.
        
        9. Download the Change-O bundle, open a terminal window, change directories
           to the download folder, and run::
        
           > pip3 install changeo-x.y.z.tar.gz
        
        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. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.
        
        4. Download the Change-O bundle, open a Command Prompt, change directories to
           the download folder, and run::
        
           > pip install changeo-x.y.z.tar.gz
        
        5. For a default installation of Python 3.4, the Change-0 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.
        
        6. 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.
        
        6. If you have trouble with the ``.py`` file associations, try adding ``.PY``
           to your ``PATHEXT`` environment variable. Also, opening a
           command prompt as Administrator and run::
        
            > assoc .py=Python.File
            > ftype Python.File="C:\Python34\python.exe" "%1" %*
        
        Release Notes
        ================================================================================
        
        Version 0.3.3:  August 8, 2016
        -------------------------------------------------------------------------------
        
        Increased ``csv.field_size_limit`` in changeo.IO, ParseDb and DefineClones
        to be able to handle files with larger number of UMIs in one field.
        
        Renamed the fields ``N1_LENGTH`` to ``NP1_LENGTH`` and ``N2_LENGTH``
        to ``NP2_LENGTH``.
        
        CreateGermlines:
        
        + Added differentiation of the N and P regions the the ``REGION`` log field
          if the N/P region info is present in the input file (eg, from the
          ``--junction`` argument to MakeDb-imgt). If the additional N/P region
          columns are not present, then both N and P regions will be denoted by N,
          as in previous versions.
        + Added the option 'regions' to the ``-g`` argument to create add the
          ``GERMLINE_REGIONS`` field to the output which represents the germline
          positions as V, D, J, N and P characters. This is equivalent to the
          ``REGION`` log entry.
        
        DefineClones:
        
        + Improved peformance significantly of the ``--act set`` grouping method in
          the bygroup subcommand.
        
        MakeDb:
        
        + Fixed a bug producing ``D_SEQ_START`` and ``J_SEQ_START`` relative to
          ``SEQUENCE_VDJ`` when they should be relative to ``SEQUENCE_INPUT``.
        + Added the argument ``--junction`` to the imgt subcommand to parse additional
          junction information fields, including N/P region lengths and the D-segment
          reading frame. This provides the following additional output fields:
          ``D_FRAME``, ``N1_LENGTH``, ``N2_LENGTH``, ``P3V_LENGTH``, ``P5D_LENGTH``,
          ``P3D_LENGTH``, ``P5J_LENGTH``.
        + The fields ``N1_LENGTH`` and ``N2_LENGTH`` have been renamed to accommodate 
          adding additional output from IMGT under the ``--junction`` flag. The new
          names are ``NP1_LENGTH`` and ``NP2_LENGTH``.
        + Fixed a bug that caused the ``IN_FRAME``, ``MUTATED_INVARIANT`` and
          ``STOP`` field to be be parsed incorrectly from IMGT data.
        + Ouput from iHMMuneAlign can now be parsed via the ``ihmm`` subcommand.
          Note, there is insufficient information returned by iHMMuneAlign to
          reliably reconstruct germline sequences from the output using
          CreateGermlines.
        
        
        ParseDb:
        
        + Renamed the clip subcommand to baseline.
        
        
        Version 0.3.2:  March 8, 2016
        -------------------------------------------------------------------------------
        
        Fixed a bug with installation on Windows due to old file paths lingering in
        changeo.egg-info/SOURCES.txt.
        
        Updated license from CC BY-NC-SA 3.0 to CC BY-NC-SA 4.0.
        
        CreateGermlines:
        
        + Fixed a bug producing incorrect values in the ``SEQUENCE`` field on the
          log file.
        
        MakeDb:
        
        + Updated igblast subcommand to correctly parse records with indels. Now 
          igblast must be run with the argument ``outfmt "7 std qseq sseq btop"``.
        + Changed the names of the FWR and CDR output columns added with 
          ``--regions`` to ``<region>_IMGT``.
        + Added ``V_BTOP`` and ``J_BTOP`` output when the ``--scores`` flag is
          specified to the igblast subcommand.
        
        
        Version 0.3.1:  December 18, 2015
        -------------------------------------------------------------------------------
        
        MakeDb:
        
        + Fixed bug wherein the imgt subcommand was not properly recognizing an 
          extracted folder as input to the ``-i`` argument.
        
        
        Version 0.3.0:  December 4, 2015
        -------------------------------------------------------------------------------
        
        Conversion to a proper Python package which uses pip and setuptools for 
        installation.
        
        The package now requires Python 3.4. Python 2.7 is not longer supported.
        
        The required dependency versions have been bumped to numpy 1.9, scipy 0.14,
        pandas 0.16 and biopython 1.65.
        
        DbCore:
        
        + Divided DbCore functionality into the separate modules: Defaults, Distance,
          IO, Multiprocessing and Receptor.
        
        IgCore:
        
        + Remove IgCore in favor of dependency on pRESTO >= 0.5.0.
        
        AnalyzeAa:
        
        + This tool was removed. This functionality has been migrated to the alakazam 
          R package.
        
        DefineClones:
        
        + Added ``--sf`` flag to specify sequence field to be used to calculate
          distance between sequences.
        + Fixed bug in wherein sequences with missing data in grouping columns
          were being assigned into a single group and clustered. Sequences with 
          missing grouping variables will now be failed.
        + Fixed bug where sequences with "None" junctions were grouped together.
          
        GapRecords:
        
        + This tool was removed in favor of adding IMGT gapping support to igblast 
          subcommand of MakeDb.
        
        MakeDb:
        
        + Updated IgBLAST parser to create an IMGT gapped sequence and infer the
          junction region as defined by IMGT.
        + Added the ``--regions`` flag which adds extra columns containing FWR and CDR
          regions as defined by IMGT.
        + Added support to imgt subcommand for the new IMGT/HighV-QUEST compression 
          scheme (.txz files).
        
        
        Version 0.2.5:  August 25, 2015
        -------------------------------------------------------------------------------
        
        CreateGermlines:
        
        + Removed default '-r' repository and added informative error messages when 
          invalid germline repositories are provided.
        + Updated '-r' flag to take list of folders and/or fasta files with germlines.
          
          
        Version 0.2.4:  August 19, 2015
        -------------------------------------------------------------------------------
        
        MakeDb:
        
        + Fixed a bug wherein N1 and N2 region indexing was off by one nucleotide
          for the igblast subcommand (leading to incorrect SEQUENCE_VDJ values).
        
        ParseDb:
        
        + Fixed a bug wherein specifying the ``-f`` argument to the index subcommand 
          would cause an error.
          
        
        Version 0.2.3:  July 22, 2015
        -------------------------------------------------------------------------------
        
        DefineClones:
        
        + Fixed a typo in the default normalization setting of the bygroup subcommand, 
          which was being interpreted as 'none' rather than 'len'.
        + Changed the 'hs5f' model of the bygroup subcommand to be centered -log10 of 
          the targeting probability.
        + Added the ``--sym`` argument to the bygroup subcommand which determines how 
          asymmetric distances are handled.
           
        
        Version 0.2.2:  July 8, 2015
        -------------------------------------------------------------------------------
        
        CreateGermlines:
        
        + Germline creation now works for IgBLAST output parsed with MakeDb. The 
          argument ``--sf SEQUENCE_VDJ`` must be provided to generate germlines from 
          IgBLAST output. The same reference database used for the IgBLAST alignment
          must be specified with the ``-r`` flag.
        + Fixed a bug with determination of N1 and N2 region positions.
        
        MakeDb:
        
        + Combined the ``-z`` and ``-f`` flags of the imgt subcommand into a single flag, 
          ``-i``, which autodetects the input type.
        + Added requirement that IgBLAST input be generated using the 
          ``-outfmt "7 std qseq"`` argument to igblastn.
        + Modified SEQUENCE_VDJ output from IgBLAST parser to include gaps inserted 
          during alignment.
        + Added correction for IgBLAST alignments where V/D, D/J or V/J segments are
          assigned overlapping positions.
        + Corrected N1_LENGTH and N2_LENGTH calculation from IgBLAST output.
        + Added the ``--scores`` flag which adds extra columns containing alignment 
          scores from IMGT and IgBLAST output.
        
        
        Version 0.2.1:  June 18, 2015
        -------------------------------------------------------------------------------
        
        DefineClones:
        
        + Removed mouse 3-mer model, 'm3n'. 
        
        
        Version 0.2.0:  June 17, 2015
        -------------------------------------------------------------------------------
        
        Initial public prerelease.  
        
        Output files were added to the usage documentation of all scripts. 
        
        General code cleanup.  
        
        DbCore:
        
        + Updated loading of database files to convert column names to uppercase.
        
        AnalyzeAa:
        
        + Fixed a bug where junctions less than one codon long would lead to a 
          division by zero error.
        + Added ``--failed`` flag to create database with records that fail analysis.
        + Added ``--sf`` flag to specify sequence field to be analyzed.
        
        CreateGermlines:
        
        + Fixed a bug where germline sequences could not be created for light chains.
        
        DefineClones:
        
        + Added a human 1-mer model, 'hs1f', which uses the substitution rates from 
          from Yaari et al, 2013.
        + Changed default model to 'hs1f' and default normalization to length for 
          bygroup subcommand.
        + Added ``--link`` argument which allows for specification of single, complete,
          or average linkage during clonal clustering (default single).
        
        GapRecords:
        
        + Fixed a bug wherein non-standard sequence fields could not be aligned. 
        
        MakeDb:
        
        + Fixed bug where the allele 'TRGVA*01' was not recognized as a valid allele.
        
        ParseDb:
        
        + Added rename subcommand to ParseDb which renames fields.
        
        
        
        Version 0.2.0.beta-2015-05-31:  May 31, 2015
        -------------------------------------------------------------------------------
        
        Minor changes to a few output file names and log field entries.
        
        ParseDb:
        
        + Added index subcommand to ParseDb which adds a numeric index field.
        
        
        Version 0.2.0.beta-2015-05-05:  May 05, 2015
        -------------------------------------------------------------------------------
        
        Prerelease for review.
        
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
