kaiko and casanovo multiple comparisons

[jynlee7]

This PR is for a script that compares multiple Kaiko and Casanovo output sequences and puts it into one tsv file.

• the script creates three functions, get_mgf_path_by_filename, get_kaiko_path_by_mgf_filename, get_casanovo_path_by_mgf_filename
• each function does what the name of it does, first get_mgf_path_by_filename, inputs mgf_paths and it turns the mgf_paths into a dictionary with the mgf_file name and the mgf_path, so the dictionary would look something like this mgf_dict: dict{'input1': 'path/to/input1.mgf', 'input2': 'path/to/input2.mgf', ...}
• get_kaiko_path_by_mgf_filename, would take in a list of kaiko output file paths, and return mgf_dict: dict{'input1': 'path/to/input1_out.txt', 'input2': 'path/to/input2_out.txt', ...}
• get_casanovo_path_by_mgf_filename, would take a list of casanovo output file paths, and return mgf_dict: dict{'input1': 'path/to/casanovo_20230710143300.mztab', 'input2': 'path/to/casanovo_20230710143400.mztab', ...}
• with these dictionaries, I created a for loop to find all of the common paths out of the 36 mgf files, and another for loop finding the common paths and outputting them into separate columns in the compare dataframe
• then saved the dataframe into the output_path above

Added Casanovo outputs of the 300k mgf files. Used the gpu in order to finish the process in an optimal amount of time.

[jynlee7]

the run_casanovo.sh was a bash script in order to run the 300k mgf files into the casanovo model to get mztab outputs

[jynlee7]

in order to run this code you need the function aggregate_kaiko_casanovo from design_comparison_table.py

[jynlee7]

@CamiloPosso, I resolved all the conflicts so that it's ready to merge.