Allow use of pipeline using only nucleotide file

[Paul Villanueva]

Pipeline currently requires a nucleotide file, a corresponding protein file, and a map file that shows which nucleotide sequence translates to which protein sequence.

Add arguments/options to the various parts of the pipeline to support the case where the user doesn't want to use the protein file.

Files affected:

• mfpsearch
  • add an argument -m/--mode that takes in n or p to indicate whether to run in nucleotide or protein mode, respectively.
  • creation of the database and the search scripts will change depending on the mode used.
• mfpprepare
  • add an argument n or p to indicate whether to run in nucleotide or protein mode, respectively.
  • if in nucleotide mode, should ignore the map argument.