Phigaro

- Restored a compatibility with Python versions `>3.7.1`.
- `.pickle` files, containing data neccasary for the work of the tool, were replaced with `.json` and `.csv` files to resolve installation issues.
- Added prophage IDs across outputs to improve compatibility between files.
- Fixed a bug with `gff3` and `bed` files formats: prophage coordinates were shifted by 1 nucleotide upstream in versions `phigaro <= 2.3.0`.

Added a `--save-fasta` option.

Minor corrections and optional temporary files saving

Minor corrections.
Docker & Singularity containers.
What_the_phage implementation.

A locate exception was added. So, if the user does not have this tool the configuration of Phigaro will not fail.

Code style: black. Output parameter corrections.