Chewbbaca

- 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.

- 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.

- Added support for genetic codes 2, 3, 5, 6, 9, 10, 12-16, 21-25 (complete list available [here](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)). 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 an 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 an issue in the AlleleCallEvaluator module related to entirely numeric columns.

- 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*.

- 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.

- 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 an 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.