Metadata-Version: 1.1
Name: changeo
Version: 0.3.12
Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Home-page: http://changeo.readthedocs.io
Author: Namita Gupta, Jason Anthony Vander Heiden
Author-email: immcantation@googlegroups.com
License: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Download-URL: https://bitbucket.org/kleinstein/changeo/downloads
Description-Content-Type: UNKNOWN
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 (Ig) sequences, and
        reconstructing germline sequences.
         
        Dramatic improvements in high-throughput sequencing technologies now enable 
        large-scale characterization of Ig repertoires, defined as the collection of
        trans-membrane antigen-receptor proteins located on the surface of B cells and
        T cells. 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
        
        The current development build can be installed using pip and mercurial in similar fashion::
        
            > pip3 install hg+https://bitbucket.org/kleinstein/changeo#default --user
        
        If you currently have a development version installed, then you will likely
        need to add the arguments ``--upgrade --no-deps --force-reinstall`` to the
        pip3 command.
        
        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 0.3.12:  February 16, 2018
        -------------------------------------------------------------------------------
        
        MakeDb:
        
        + Fixed a bug wherein specifying multiple simultaneous inputs would cause
          duplication of parsed pRESTO fields to appear in the second and higher
          output files.
        
        
        Version 0.3.11:  February 6, 2018
        -------------------------------------------------------------------------------
        
        MakeDb:
        
        + Fixed junction inferrence for igblast subcommand when J region is
          truncated.
        
        
        Version 0.3.10:  February 6, 2018
        -------------------------------------------------------------------------------
        
        Fixed incorrect progress bars resulting from files containing empty lines.
        
        DefineClones:
        
        + Fixed several bugs in the chen2010 and ademokun2011 methods that caused them
          to either fail or incorrectly cluster all sequences into a single clone.
        + Added informative message for out of memory error in chen2010 and
          ademokun2011 methods.
        
        
        Version 0.3.9:  October 17, 2017
        -------------------------------------------------------------------------------
        
        DefineClones:
        
        + Fixed a bug causing DefineClones to fail when all are sequences removed from
          a group due to missing characters.
        
        
        Version 0.3.8:  October 5, 2017
        -------------------------------------------------------------------------------
        
        AlignRecords:
        
        + Ressurrected AlignRecords which performs multiple alignment of sequence
          fields.
        + Added new subcommands ``across`` (multiple aligns within columns),
          ``within`` (multiple aligns columns within each row), and ``block``
          (multiple aligns across both columns and rows).
        
        CreateGermlines:
        
        + Fixed a bug causing CreateGermlines to incorrectly fail records when using
          the argument ``--vf V_CALL_GENOTYPED``.
        
        DefineClones:
        
        + Added the ``--maxmiss`` argument to the bygroup subcommand of DefineClones
          which set exclusion criteria for junction sequence with ambiguous and
          missing characters. By default, bygroup will now fail all sequences
          with any missing characters in the junction (``--maxmiss 0``).
        
        
        Version 0.3.7:  June 30, 2017
        -------------------------------------------------------------------------------
        
        MakeDb:
        
        + Fixed an incompatibility with IgBLAST v1.7.0.
        
        CreateGermlines:
        
        + Fixed an error that occurs when using the ``--cloned`` with an input file
          containing duplicate values in ``SEQUENCE_ID`` that caused some records to
          be discarded.
        
        
        Version 0.3.6:  June 13, 2017
        -------------------------------------------------------------------------------
        
        + Fixed an overflow error on Windows that caused tools to fatally exit.
        + All tools will now print detailed help if no arguments are provided.
        
        
        Version 0.3.5:  May 12, 2017
        -------------------------------------------------------------------------------
        
        Fixed a bug wherein ``.tsv`` was not being recognized as a valid extension.
        
        MakeDb:
        
        + Added the ``--cdr3`` argument to the igblast subcommand to extract the
          CDR3 nucleotide and amino acid sequence defined by IgBLAST.
        + Updated the IMGT/HighV-QUEST parser to handle recent column name changes.
        + Fixed a bug in the igblast parser wherein some sequence identifiers were
          not being processed correctly.
        
        DefineClones:
        
        + Changed the way ``X`` characters are handled in the amino acid Hamming
          distance model to count as a match against any character.
        
        
        Version 0.3.4:  February 14, 2017
        -------------------------------------------------------------------------------
        
        License changed to Creative Commons Attribution-ShareAlike 4.0 International
        (CC BY-SA 4.0).
        
        CreateGermlines:
        
        + Added ``GERMLINE_V_CALL``, ``GERMLINE_D_CALL`` and ``GERMLINE_J_CALL``
          columns to the output when the ``-cloned`` argument is specified. These
          columns contain the consensus annotations when clonal groups contain
          ambiguous gene assignments.
        + Fixed the error message for an invalid repo (``-r``) argument.
        
        DefineClones:
        
        + Deprecated ``m1n`` and ``hs1f`` distance models, renamed them to
          ``m1n_compat`` and ``hs1f_compat``, and replaced them with ``hh_s1f`` and
          replaced ``mk_rs1nf``, respectively.
        + Renamed the ``hs5f`` distance model to ``hh_s5f``.
        + Added the mouse specific distance model ``mk_rs5nf`` from Cui et al, 2016.
        
        MakeDb:
        
        + Added compatibility for IgBLAST v1.6.
        + Added the flag ``--partial`` which tells MakeDb to pass incomplete alignment
          results specified.
        + Added missing console log entries for the ihmm subcommand.
        + IMGT/HighV-QUEST, IgBLAST and iHMMune-Align parsers have been cleaned up,
          better documented and moved into the iterable classes
          ``changeo.Parsers.IMGTReader``, ``change.Parsers.IgBLASTReader``, and
          ``change.Parsers.IHMMuneReader``, respectively.
        + Corrected behavior of ``D_FRAME`` annotation from the ``--junction``
          argument to the imgt subcommand such that it now reports no value when no
          value is reported by IMGT, rather than reporting the reading frame as 0 in
          these cases.
        + Fixed parsing of ``IN_FRAME``, ``STOP``, ``D_SEQ_START`` and ``D_SEQ_LENGTH``
          fields from iHMMune-Align output.
        + Removed extraneous score fields from each parser.
        + Fixed the error message for an invalid repo (``-r``) argument.
        
        
        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
