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.

v3.3.3

• Fixed warning related with BLASTp --seqidlist parameter. For BLAST>=2.9, the TXT file with the sequence IDs is converted to binary format with blastdb_aliastool.

• The Bio.Application modules are deprecated and might be removed from future Biopython versions. Modified the function that calls MAFFT so that it uses the subprocess module instead of Bio.Align.Applications.MafftCommandline. Changed the Biopython version requirement to >=1.79.

• Added a pyproject.toml configuration file and simplified the instructions in setup.py. The use of setup.py as a command line tool is deprecated and the pyproject.toml configuration file allows to install and build packages through the recommended method.

• Updated the Dockerfile to install chewBBACA with python3 -m pip install . instead of the deprecated python setup.py install command.

• Removed FASTA header integer conversion before running BLASTp. This was done to avoid a warning from BLAST related to sequence header length exceeding 50 characters.

• The seqids and coordinates of the CDSs closest to contig tips are stored in a dictionary during gene prediction to simplify LOTSC and PLOT5/3 determination (in many cases this reduces runtime by ~20%).

• Limited the number of values stored in memory while creating the results_contigsInfo.tsv and results_alleles.tsv output files to reduce memory usage.

• Adding data to the FASTA and TSV files for the missing classes per locus instead of storing the complete per input data to reduce memory usage.

• The data for novel alleles is saved to files to reduce memory usage.

• Fixed the in-frame stop codon count values displayed in the reports created by the SchemaEvaluator module.

• The UniprotFinder module now exits cleanly if the output directory already exists.

• Improved info printed to the stdout by the CreateSchema and AlleleCall modules, added comments, and changed variable names to better match data being stored.

v3.3.2

• Changed FASTA file validation to reduce memory usage.

• Removed legacy schema conversion. Users should use the PrepExternalSchema module to adapt schemas created with chewBBACA<=2.1.0.

• Added prints about output files created by the PrepExternalSchema module.

v3.3.1

• Fixed issue leading to errors during allele calling if it was running in default mode (4) and all CDSs were classified before representative determination.

• Fixed schema name assignment in the DownloadSchema module.

• Fixed bug related to gene prediction parallelization when running Pyrodigal in meta mode.