Translate gene

[jpjarnoux]

Two things have been done here:

1. Added the ability to write the translated sequence of all genes using MMSeqs2 with the --genes_prot option, which works like the other options in the ppanggolin fasta command.
2. In MSA, if the gene sequence length was not divisible by 3, PPanGGOLiN raised an error. To be more flexible, the last one or two nucleotides are deleted if the sequence size is not modulo 3. A warning message is issued if necessary to inform the user.

[jpjarnoux]

MMseqs2 create db must be forced in mode 1. So in translate_genes we must force the mode.

[axbazin]

This is very similar to "translate_with_mmseqs" in the "align" module, maybe we can replace the "translate_with_mmseqs" with this function as well to centralize "translation" in ppanggolin?

[axbazin]

And you talked about it already, but removing genetic_codes.py is definitely a good idea if we don't use it anymore