v3.4.2

• Fixed issue in the ExtractCgMLST module related to using the deprecated Plotly titlefont attribute. Support for the titlefont attribute was dropped in Plotly v6.0.0. The ExtractCgMLST module would exit with an error and fail to generate the HTML plot if Plotly >= v6.0.0 was installed.

• The LoadSchema module no longer queries UniProt's SPARQL endpoint to retrieve annotations. The current implementation was failing to retrieve annotations. Users should use the UniprotFinder module or the annotation functionalities provided by Schema Refinery to annotate the schema loci and create a TSV file with annotations to submit to Chewie-NS.

v3.4.1

• Changed the -max_target_seqs value used by the select_representatives function to the square of the number of potential new representative alleles or to a minimum of 100. This change tries to fix an issue where BLASTp would not report the self-alignment for some alleles because it reached the limit of the number of alignments to report before reporting all self-alignments (e.g. for very large datasets, the number of potential new representatives may lead to a number of alignments that exceeds the value passed to -max_target_seqs).

v3.4.0

• Add the GetAlleles module to create FASTA files containing the alleles identified by the AlleleCall module.

v3.3.10

• Fixed issue in the UniprotFinder module related to TrEMBL and Swiss-Prot IDs being parsed by BLAST when the qacc and sacc format specifiers were used with -outfmt 6. Switched back to the qseqid and sseqid format specifiers.

v3.3.9

• Fixed an issue related to sequence IDs interpreted by BLAST as PDB chain IDs.

• Fixed an issue related to CDS counting when gene prediction returns no CDSs for one or more inputs.

v3.3.8

• Added support for genetic codes 2, 3, 5, 6, 9, 10, 12-16, 21-25 (complete list available here). Values passed to --t, --translation-table are ignored if a training file is used. The CreateSchema, AlleleCall and PrepExternalSchema modules use the genetic code used to create the training file.

• Fixed issue related to data about CDSs close to the contig tips not being available if input FASTA files contain CDSs and --cds is used.

• Fixed issue in the AlleleCallEvaluator module related to entirely numeric columns.

v3.3.7

• Fixed issue in the PrepExternalSchema module related to the adaptation of small loci (BLASTp would not report the self-alignment).

• Added training file for Pseudomonas aeruginosa.

v3.3.6

• Added support for translation tables different than 11 to UniprotFinder and AlleleCallEvaluator.

• Added check for legacy schemas that include files terminating in bsr.txt. The AlleleCall module warns users that the schema needs to be adapted and exits.

• Changed the max_targets value in UniprotFinder to avoid BLASTp warning when aligning schema representative alleles against proteomes.

• Fixed an issue in the AlleleCallEvaluator module when using --no-pa and --no-dm.

• The AlleleCallEvaluator module no longer tries to compute the distance matrix, MSA, and tree if the cgMLST is composed of 0 loci.

• Fixed an issue in RemoveGenes where it would not get the first ID in the input list.

• Updated Dockerfile. Using pip to install chewBBACA instead of downloading source from GitHub.

v3.3.5

• Added function to check if input files passed to the CreateSchema and AlleleCall modules have unique prefixes longer than 30 characters (the prefix includes everything in the basename before the first .). The process prints a message with the list of input files with a prefix longer than 30 characters and exits.

• Fixed issue in the AlleleCall module when running in mode 1 (trying to write the file with the list of invalid CDSs, but the data is not available when running in mode 1).

• Added more tests and improved test scripts.

• Simplified the help message for all modules.

v3.3.4

• Improved BLAST exception capturing.

• CreateSchema and Allelecall exit if input files include blank spaces in the filename.

• Removed global variable that could lead to issues during multiprocessing.