v1.7.4

• Adds --trna_scan_model parameter with two accepted options: --trna_scan_model general (this will be run by default - what Pharokka has always been running) and --trna_scan_model bacterial. See the tRNAscan-SE paper for more information about their models.
• Bumps the dnaapler dependency to v1.0.1 due to a breaking dependency change in dnaapler.

v1.7.3

• Fixes issue with genbank creation if certain CARD hits are found #339
  • Due to some semi-colons in the CARD metadata, new qualifier keys were being made in error.
  • Solved by removing semicolons in the updated CARD metadata sheet

v1.7.2

• Identifies issue if # is input contig header - Pharokka will error if your contig headers contain this character and prompt you to remove them. #300

v1.7.1

• Adds Google Colab notebook that can run pharokka and phold.
• The notebook is https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold.ipynb
• Fixes #334 issue with contig ids if they were in scientific notation or lead with 0s.
• Fixes issues with pharokka_proteins.py not outputting PHROG annotations.

v1.7.0

• Adds pharokka_multiplotter.py to plot multiple phage contigs at once #326
• Adds separate contig FASTA files to the output if -s -m is specified (in single_fastas)

v1.6.1

Patch release to fix a bug introduced in v1.6.0 that was removing tRNAs from the .tbl output format #323

v1.6.0

• Fixes a variety of bugs (#300 pharokka_proteins.py crashing if it found VFDB hits, #303 errors in the .tbl format, #316 errors with types and where custom HMM dbs had identical scored hits, #317 types (e.g. where the contig header was a integer) and #320 deprecated GC function)
• Adds --mash_distance and --minced_args as parameters (#299 thanks @iferres).
• Enforces Biopython < 1.82

v1.5.1

1.5.1 (2023-10-26)

• Fixes dnaapler version to >=0.4.0 with new changes to dnaapler
• Adds .svg format output with pharokka_plotter.py

v1.5.0

• Adds support for pyrodigal-gv implementing prodigal-gv as a gene predictor (pyrodigal-gv and prodigal-gv). This can be specified with -g prodigal-gv.
• Thanks to @althonos and @apcamargo for making this possible, and to @asierFernandezP for raising this as an issue in the first place here in #290.
• Adds checks to determine if your input FASTA has duplicated contig headers from #293 here. Thanks @thauptfeld for raising this.
• -g prodigal and -g prodigal-gv should be much faster thanks to multithread support added by the inimitable @althonos.
• Genbank format output will be designated with PHG not VRL (following this issue RyanCook94/inphared#22).
• The _length_gc_cds_density.tsv and _cds_final_merged_output.tsv files now contain the translation table/genetic code for each contig (usually 11 but now not always if you use pyrodigal-gv).
• --skip_mash flag added to skip finding the closest match for each contig in INPHARED using mash.
• --skip_extra_annotations flag added to skip running tRNA-scanSE, MinCED and Aragorn in case you only want CDS predictions and functional annotations.

v1.4.1

1.4.1 (2023-09-04)

Pharokka v1.4.1 is a small patch fix release fixing #286, where if you specified --dnaapler and -m, pharokka would not find the correct output file from dnaapler and would crash.

Thanks for spotting the bug @rdenise.

Full Changelog: v1.4.0...v1.4.1