Add option to input GFF and protein FASTA, and output prot_ids

[pentamorfico]

Added support for parsing Prodigal/Prokka/Bakta GFFs 8880c6a.

A few notes:

• The added lines initially attempt to identify the "protein_id" label in the attributes, which is a characteristic of NCBI GFFs.
• If "protein_id" is not found, it then tries to retrieve the "ID" label from the attributes, a feature seen in Prodigal, Prokka, and Bakta.
• It further inspects whether the ID values adhere to either the ...XXXX_1234... format (seen in Prokka and Bakta) or the ..1234_1234... format (observed in Prodigal).
• If the IDs conform to Prokka or Bakta's format, they are retained as is. If not, the IDs are altered in Prodigal by replacing everything before the "_" with the contig name found in the first column.
• By default, Bakta modifies the names of the contigs to follow the pattern "contig_1", "contig_2", and so on. Therefore, either the FNA input generated by Bakta should be used as an input (with the modified IDs) or the GFF Contig column should be renamed to match those of the original FNA file.