subcommand find/rename

[ammaraziz]

subcommand find/rename

[ammaraziz]

For the rename branch to be merged into main, I need to fix or add the following:

• The controls for how headers are renamed (add_month, add_gene, add_passage) is hidden under a single flag rename. Should these be exposed?
• Handle if the date is missing
• Handle if the designation is missing
• output unmatched records and print this to terminal
• fix the issue with spaces not being replaced with _.
• Handle ascii character ' -> replace with nothing ''
• There's an issue with write_sequences, it expects a dict which works for when sequences are renamed. If they are not renamed, a list is given to write_sequences. Two options, write_sequences detects the object type and acts accordingly or a new function needs to be written.