Pharokka

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

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* Adds `pharokka_multiplotter.py` to plot multiple phage contigs at once
* Adds separate contig FASTA files if `-s -m` is run (in `single_fastas`)

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* Fixes a bug that was removing tRNAs from the `.tbl` output format 323.

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* 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 and 320 deprecated GC function)
* Adds `--mash_distance` and `--minced_args` as parameters (299 thanks iferres).

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

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* Adds support for `pyrodigal-gv` implementing `prodigal-gv` as a gene predictor ([pyrodigal-gv](https://github.com/althonos/pyrodigal-gv) and [prodigal-gv](https://github.com/apcamargo/prodigal-gv)). This can be specified with `-g prodigal-gv`.
* Thanks to [althonos](https://github.com/althonos) and [apcamargo](https://github.com/apcamargo) for making this possible, and to [asierFernandezP](https://github.com/asierFernandezP) for raising this as an issue in the first place [here](https://github.com/gbouras13/pharokka/issues/290) in #290.
* Adds checks to determine if your input FASTA has duplicated contig headers from 293 [here](https://github.com/gbouras13/pharokka/issues/293). Thanks [thauptfeld](https://github.com/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 https://github.com/RyanCook94/inphared/issues/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.