Release Notes

CHanges in 0.8.1

  • Revised motif tables to fully implement the new Max/Min values for RSS spacers

Changes in 0.8.0

  • Breaking change: the motif file ‘motif_params.json’ now takes minimum and maximum RSS spacings for V, D and J RSS, to allow tuning/exploration. If you have a custom motif_params.json file, you will need to update it to the new format. Note that, by default, Digger has always provided 1nt of flexibility in V and J RSS spacing, eg 22-23, 11-12. This was previously built into the code, but now needs to be specified in the motif_params.json file. For examples of the new format, see github.

  • Added new exon annotation columns: exon1, exon1_start, exon1_start_rev, exon1_end, exon1_end_rev and corresponding columns for exon 2

  • Added new RSS annotation columns: v_spacer, v_spacer_length, j_spacer, j_spacer_length, d_3_spacer, d_3_spacer_length, d_5_spacer, d_5_spacer_length

  • Added new leader splice columns: donor-splice, acceptor-splice

  • Revised annotation of L-PART1 to match IMGT convention (see V Leader Annotation for details).

  • Breaking change: REMOVED coordinate columns for l-part1, l-part2 - see above for why.

Changes in 0.7.7

  • The donor splice (GT) is no longer included in the annotation of L-PART1. This is a break in custom with IMGT, who typically include the GT in the L-PART1 annotation. However, this means that L-PART1 and L-PART2 now exactly match the exon, which we feel is important for clarity. To enable the donor splice to be examined more easily, Digger now explicitly annotates the V intron.

  • Fix erroneous ‘failed coordinate check’ messages which were emitted where an annotated region extends beyond the assembly boundaries.

Changes in 0.7.6

  • fix problem in handling multiple contigs

Changes in 0.7.5

  • further salmonid name fix

Changes in 0.7.4

  • fix problem with salmonid names, e.g. TRB3V

Changes in 0.7.3

  • fix crash in compare_annotations.py

Changes in 0.7.2

  • digger will default to using the starting set of reference genes for comparison, if no sets are specified with -ref_comp.

Changes in 0.7.1

  • digger will now copy reference set files to the work directory if necessary, as blast’s makedb requires the files to be local.

  • digger can now handle multiple sequences (e.g. contigs) in the assembly file.

Changes in 0.7.0

  • modify motif handling to allow multiple motifs in those cases where the length can be variable

  • add variable length motifs for l-part1 and l-part2

  • motifs are now based on the analysis in tests/utr

  • add identification of TATA_BOX and OCTAMER in promoter regions

Changes in 0.6.9

  • bump dependency on receptor-utils to fix an issue with naming of D novel alleles

Changes in 0.6.8

  • improve documentation, add additional examples in tests, add Dockerised version

  • include TRG motif files in the package

Changes in 0.6.7

  • include motif files for TRG

Changes in 0.6.7

  • better error handling and explanation in parse_imgt_annotations

  • Docker image added

Changes in 0.6.6

  • fix crash in dig_sequence if annotating V-gene without specifying a gapped reference file

  • update the package to include missing motif files

Changes in 0.6.4

  • fix issue in dig_sequence

Changes in 0.6.3:

  • add support for multiple definitions of the J motif for a locus

  • move J-TRP and other motif definitions to a file in the motifs directory

Changes in 0.6.2:

  • require the user to supply an email address for requests to GenBank.

Changes in 0.6.1:

  • bump required version of receptor-utils

Changes in 0.6.0:

  • added support for TRA, TRB, TRD, TRG and test cases and motifs for human TR loci

Changes in v 0.5.10:

  • fixed unintended breakpoint in find_alignments which could fire under some circumstances

Changes in v 0.5.9:

  • fixed erroneous reporting of leader1 sequence and co-ordinates when leader1 was not included in the query sequence

Changes in v 0.5.8:

  • fixed various issues with end effects leading to the reporting of negative coordinates

  • fixed an issue with targeted annotation which caused negative sense not to be properly reported

  • changed IMGT urls to use https as http is no longer utilised

Changes in v 0.5.7:

  • modified reporting of nt_diff so that it reports the number of nt differences between the query and the reference, including any length differences.

  • updated the code to use Bio.Align rather than Bio.pairwise2, which is deprecated.

Changes in v 0.5.6:

  • compatibility update for receptor_utils 0.0.40

Changes in v 0.5.5:

  • speed optimisation for dig_sequence

  • allow find_alignments to be called without a -ref parameter

Changes in V 0.5.4:

  • Minor fixes to handling of non-functional sequences

Changes in V 0.5.3:

  • Fixes to annotation in reverse-sense: false positives were not being filtered correctly

Changes in V 0.5.2:

  • Added dig_sequence command, which allows a sequence stored locally or in Genbank to be searched for a specific allele. The closest match will be annotated.

Changes in V 0.5.1:

  • Refactored elements of the code to make it more modular and easier to maintain.

Version 0.5: April 2023

First public version.