-h, --help      show this help message and exit
-i INPUT_FILES  Path to a FASTA file with contig sequences for a single
                genome.
-o OUTPUT_PATH  Path to the directory that will store output files created
                by the process.
-s sample_metadata path to samplemetadata (TSV file containing fastafile name, species, codon number.
--bsr BSR       BLAST Score Ratio value used as threshold.
--t THREADS     Number of threads used by BLASTp to align translated genes.
--p probabbility probability change of a gene found by Augsustus, used as an cutoff

--add_loci path path to fasta file containing the CDS of each gene in it. This parameters enables to directly add genes to a folder containing all genes
--codon Required codon table number to calculate the AA sequence of the CDS
--force Forces the genes from the add_loci parameter to be directly added to the clustering dir (genes will have a forced prefix)
-o OUTPUT_PATH  Path to the directory that will store output files created
                by the process.

--add_gene path to directory containing the fastafiles of genomes to be added to processed genomes
-s sample_metadata path to samplemetadata (TSV file containing fastafile name, species, codon number.
-o OUTPUT_PATH  Path to the directory that will store output files created
                by the process.
-recluster If recluster = True, after adding the gene, all known genes will be directly evaluated by Clustering and blasting to retrieve the 
--bsr BSR       BLAST Score Ratio value used as threshold.
--t THREADS     Number of threads used by BLASTp to align translated genes.
--p probabbility probability change of a gene found by Augsustus, used as an cutoff

python3 euTyper.py -i /path/to/your/favourite/directory/containing/genomes -o /output/folder/path/of/directory/be/created/and/files/stored -s /path/to/sample_metadata --t 30 --p 0.9

python3 euTyper.py -add_loci /path/to/your/favourite/directory/containing/genes -o --t 30 --codon 12 --forced True 

python3 euTyper.py -add_gene /path/to/your/favourite/directory/containing/genomes -o /output/folder/path/of/directory/be/created/and/files/stored -s /path/to/sample_metadata --t 30 --p 0.7 -recluster True

python3 euTyper.py --reclyster -o  /output/folder/path/of/directory/be/created/and/files/stored --t 20

python3 euTyper.py -o /output/folder/path/of/directory/be/created/and/files/stored --t 30 -s /path/to/sample_metadata -i //path/to/your/favourite/directory/containing/genomes --p 0.5 --re_use_augustus /work/directory/of/already/processed/euTyper