Pharokka

------------------

* Minor update to fix Biopython version <=1.80, due to a breaking change with 1.81 and bcbio-gff this [issue](https://github.com/chapmanb/bcbb/issues/136).

------------------

* Adds the functionality of mapping each contig against the INPHARED database using mash (https://github.com/RyanCook94/inphared). The top hit for each contig (under a maximum mash distance threshold of 0.2) is kept.
* New database adding INPHARED.
* Replaced prodigal with pyrodigal as it is being actively maintained and used by bakta.
* Adds --citation.
* Adds checks for dependencies.
* Adds --terminase terminase mode to re-orient a single contig phage to begin with a certain orientation and coordinate (most commonly, the large terminase subunit). With this, you must also specify --terminase_strand the strand of the terL gene and --terminase_start the start coordinate.
* All locus tags end with 4 digits (trailing zeros) in order to play nice with vConTACT2 and start with 1 not 0.
* In meta mode, the locus tags now begin with the contig header, not a random string (or chosen prefix).
* Cleans up the .tbl so it should automatically be accepted by NCBI Bankit.

------------------

* Renames the CDS output files to *.faa for amino acids and *.ffn for nulceotide sequences
* Implementation of consistent CDS name (equal to the locus_tag) across all output files
* Creates terL.faa and terL.ffn, which contain the sequences of any identified terminase large subunit CDSs
* Passes multithreading to PHANOTATE and tRNAscan-SE in meta mode indicated by flag -m, which provides approximately a t-fold improvement in run-time for large metavirome datasets, where t is the number of threads.

------------------

* Minor release to fix a string-parsing bug where pharokka v1.0.0 would crash when certain VFDB virulence factors were detected.

------------------

* Removes errors (with post_processing functions not being parsed as strings) to improve robustness.
* Codebase more reliable and consistent
* Overhaul of install_databases.py
* Adds pre-existing Pharokka Database available at https://zenodo.org/record/7081772

------------------

* Adds CARD and VFDB databases.