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A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.

Project 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.

Linux

  1. The simplest way to install all Python dependencies is to install the full SciPy stack using the instructions, then install Biopython according to its instructions.

  2. Install presto 0.5.0 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.

  2. Older versions Mac OS X will require you to install XQuartz 2.7.5. Available from the XQuartz project.

  3. Install Homebrew following the installation and post-installation instructions.

  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 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, 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 collection.

  3. Install presto 0.5.0 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.

  1. 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 0.3.8: 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.

Release History

Release History

This version
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0.3.8

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0.3.7

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0.3.6

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0.3.5

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0.3.4

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0.3.3

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0.3.2

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0.3.1

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0.3.0

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