"Read the whole document (each column). Default is only the first column.",
action="store_true")
parser.add_argument("--skip", help="Skip the every nth column", default=0)
args = parser.parse_args()
theoretical_name = args.theoretical
observed_name = args.observed
output_name = args.output_csv
is_separate = args.separate_species
tolerance = float(args.tolerance)
order = args.order
whole = args.whole
skip = int(args.skip)
species = sr.json_to_species(theoretical_name)
ions = [mol for mol in species if mol.category == "Ion"]
adducts = [mol for mol in species if mol.category == "Adduct"]
modifications = [mol for mol in species if mol.category == "Modification"]
print(len(ions), "ions,", len(adducts), "adducts,", len(modifications),
"modifications.")
theoretical_spectrum = TheoreticalSpectrum(ions, adducts, modifications)
with open(observed_name) as csv_file:
csv_reader = csv.reader(csv_file, delimiter=";")
observed_spectrum = []
for row in csv_reader:
if whole:
observed_spectrum.append([process_cell(cell) for cell in row])
else:
def test_json_to_species(self):
species = sr.json_to_species("data/species_rule.json")
print([s.species() for s in species])