options:
  -h, --help            show this help message and exit
  -wDir WDIR            Working directory for fasta files and output folder
  -geneFile GENEFILE    Input all gene sequences including backbone in a fasta format. Place all in one fasta file.
                        Name description can include start and end points (>gene1 start:1 end:2)
  -handle HANDLE        Genetic handle for domain insertion. This is important for defining the linker. Currently
                        uses BsaI (4 base overhang), but this can be swapped for SapI (3 base overhang).
  -dis DIS              use the handle to insert domains at every position in POI
  -matchSequences       Find similar sequences between genes to avoid printing the same oligos multiple times.
                        Default: No matching
  -oligoLen OLIGOLEN    Synthesized oligo length
  -fragmentLen FRAGMENTLEN
                        Maximum length of gene fragment
  -overlap OVERLAP      Enter number of bases to extend each fragment for overlap. This will help with insertions
                        close to fragment boundary
  -DMS                  Choose if you will run deep deep mutation scan
  -custom_mutations CUSTOM_MUTATIONS
                        Path to file that includes custom mutations with the format position:AA
  -usage USAGE          Default is "human". Or select "ecoli. Or change code"
  -insertions INSERTIONS [INSERTIONS ...]
                        Enter a list of insertions (nucleotides) to make at every position. Note, you should enter
                        multiples of 3 nucleotides to maintain reading frame
  -deletions DELETIONS [DELETIONS ...]
                        Enter a list of deletions (number of nucleotides) to symmetrically delete (it will make
                        deletions in multiples of 2x). Note you should enter multiples of 3 to maintain reading
                        frame
  -include_substitutions INCLUDE_SUBSTITUTIONS
                        If you are running DMS but only want to insert or delete AA
  -barcode_start BARCODE_START
                        To run DIMPLE multiple times, you will need to avoid using the same barcodes. This allows
                        you to start at a different barcode.
  -restriction_sequence RESTRICTION_SEQUENCE
                        Recommended using BsmBI - CGTCTC(G)1/5 or BsaI - GGTCTC(G)1/5
  -avoid_sequence AVOID_SEQUENCE [AVOID_SEQUENCE ...]
                        Avoid these sequences in the backbone - BsaI and BsmBI. For multiple sequnces use a space
                        between inputs. Example -avoid_sequence CGTCTC GGTCTC
  -include_stop_codons  Include stop codons in the list of scanning mutations.
  -include_synonymous   Include synonymous codons in the list of scanning mutations.
  -make_double          Make each combination of mutations within a fragment

Run the GUI with the commandline prompt: python run_dimple_gui.py

You must select:
  -Target Gene File - select fasta file with name description including start and end points (>gene1 start:1 end:2)
  -One or more of the mutations to make to the target gene
  
 Run the program by pressing Run DIMPLE