Release Notes

Version 0.4.2: September 6, 2018

  • Updated support for the AIRR Rearrangement schema to v1.2 and added the associated airr library dependency.

AssignGenes:

  • New tool.
  • Provides a simple IgBLAST wrapper as the igblast subcommand.

ConvertDb:

  • The genbank subcommand will perform a check for some of the required columns in the input file and exit if they are not found.
  • Changed the behavior of the -y argument in the genbank subcommand. This argument is now featured to sample features only, but allows for the inclusion of any BioSample attribute.

CreateGermlines:

  • Will now perform a naive verification that the reference sequences provided to the -r argument are IMGT-gapped. A warning will be issued to standard error if the reference sequence fail the check.
  • Will perform a check for some of the required columns in the input file and exit if they are not found.

MakeDb:

  • Changed the output of SEQUENCE_VDJ from the igblast subcommand to retain insertions in the query sequence rather than delete them as is done in the SEQUENCE_IMGT field.
  • Will now perform a naive verification that the reference sequences provided to the -r argument are IMGT-gapped. A warning will be issued to standard error if the reference sequence fail the check.

Version 0.4.1: July 16, 2018

  • Fixed installation incompatibility with pip 10.
  • Fixed duplicate newline issue on Windows.
  • All tools will no longer create empty pass or fail files if there are no records meeting the appropriate criteria for output.
  • Most tools now allow explicit specification of the output file name via the optional -o argument.
  • Added support for the AIRR standard TSV via the --format airr argument to all relevant tools.
  • Replaced V, D and J BTOP columns with CIGAR columns in data standard.
  • Numerous API changes and internal structural changes to commandline tools.

AlignRecords:

  • Fixed a bug arising when space characters are present in the sequence identifiers.

ConvertDb:

  • New tool.
  • Includes the airr and changeo subcommand to convert between AIRR and Change-O formatted TSV files.
  • The genbank subcommand creates MiAIRR compliant files for submission to GenBank/TLS.
  • Contains the baseline and fasta subcommands previously in ParseDb.

CreateGermlines

  • Changed character used to pad clonal consensus sequences from . to N.
  • Changed tie resolution in clonal consensus from random V/J gene to alphabetical by sequence identifier.
  • Added --df and -jf arguments for specifying D and J fields, respectively.
  • Add initial sorting step with specifying --cloned so that clonally ordered input is no longer required.

DefineClones:

  • Removed the chen2010 and ademokun2011 and made the previous bygroup subcommand the default behavior.
  • Renamed the --f argument to --gf for consistency with other tools.
  • Added the arguments --vf and -jf to allow specification of V and J call fields, respectively.

MakeDb:

  • Renamed --noparse argument to --asis-id.
  • Added asis-calls argument to igblast subcommand to allow use with non-standard gene names.
  • Added the GERMLINE_IMGT column to the default output.
  • Changed junction inference in igblast subcommand to use IgBLAST’s CDR3 assignment for IgBLAST versions greater than or equal to 1.7.0.
  • Added a verification that the SEQUENCE_IMGT and JUNCTION fields are in agreement for records to pass.
  • Changed behavior of the igblast subcommand’s translation of the junction sequence to truncate junction that are not multiples of 3, rather than pad to a multiple of 3 (removes trailing X character).
  • The igblast subcommand will now fail records missing the required optional fields subject seq, query seq and BTOP, rather than abort.
  • Fixed bug causing parsing of IgBLAST <= 1.4 output to fail.

ParseDb:

  • Added the merge subcommand which will combine TSV files.
  • All field arguments are now case sensitive to provide support for both the Change-O and AIRR data standards.

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.