test_regex.py

import re

# Define the regexes
regex_dict = {}
regex_dict['regex_wt'] = '\+'
regex_dict['regex_deletion'] = '\u0394'
regex_dict['regex_partial_deletion_kept'] = '\(((?<!\d)\d+-\d+,?)+(?<!,)\)'
regex_dict['regex_partial_deletion_removed'] = '\u0394' + regex_dict['regex_partial_deletion_kept']
regex_dict['regex_delins'] = '-((?<=[,-])[A-Z]+\d+[A-Z*]+,?)+(?<!,)'
regex_dict['regex_delins_no_dash_no_commas'] = '([A-Z]+\d+[A-Z*]+)'

# Below we re-use the regexes above to define more complex regexes

# This combination is mentioned in the text of the paper
regex_dict['regex_delins_and_partial_deletion'] = '({}|{}){}'.format(regex_dict['regex_partial_deletion_kept'], regex_dict['regex_partial_deletion_removed'], regex_dict['regex_delins'])

first_composed_regex = '({}|{}|{})'.format(regex_dict['regex_partial_deletion_removed'], regex_dict['regex_partial_deletion_kept'], regex_dict["regex_delins"])
second_composed_regex = '({}|{}|{})'.format(regex_dict['regex_partial_deletion_removed'], regex_dict['regex_delins_no_dash_no_commas'], regex_dict["regex_deletion"])
regex_dict['regex_CTD'] = '{}?-CTD-((?<=[,-]){}(\(r\d+-r\d+(-\d+)?\))?,?)+(?<!,)'.format(first_composed_regex, second_composed_regex)

print('\u03A8 in table legend:', first_composed_regex)
print('\u03A9 in table legend:', second_composed_regex)

# Define the test cases
cases_dict = {}
cases_dict['regex_wt'] = ['ase1+']
cases_dict['regex_deletion'] = ['ase1\u0394']
cases_dict['regex_partial_deletion_kept'] = ['ase1(10-200)', 'ase1(10-200,300-400)']
cases_dict['regex_partial_deletion_removed'] = ['ase1\u0394(10-200)', 'ase1\u0394(114-120,150-200)']
cases_dict['regex_delins'] = ['ase1-P114PVPAL', 'ase1-P114A,Q117A', 'ase1-P114*', 'ase1-PLI114AAA', 'ase1-PLI114LAVKK']
cases_dict['regex_delins_and_partial_deletion'] = ['ase1(10-200)-P224A,Q337A,L400*', 'ase1\u0394(10-200)-P224A,Q337A,L400*']
cases_dict['regex_CTD'] = ['ase1-CTD-Y1F',
                            'ase1-CTD-Y1F(r1-r12)',
                            'ase1-CTD-\u0394(r11-r29)',
                            'ase1-CTD-Y1F(r1-r29-2)',
                            'ase1-CTD-S5A(r1-r12),\u0394(r13-r29)',
                            'ase1\u0394(1-100)-CTD-\u0394(r11-r29)',
                            'ase1-N494D-CTD-\u0394(r11-r29)',
                            'ase1-S2A,N494D-CTD-Y1F,S5A(r11-r29),\u0394(r11-r29)']


# Switch case on the keys of regex_dict
for key in cases_dict:
    # Switch case on the values of cases_dict
    for value in cases_dict[key]:
        # Test if the regex matches the value
        assert re.fullmatch('ase1' + regex_dict[key], value) is not None, f'{value} does not match {regex_dict[key]}'

# cases that should fail

cases_dict = {}
cases_dict['regex_wt'] = ['ase1++']
cases_dict['regex_deletion'] = ['ase1D']
cases_dict['regex_partial_deletion_kept'] = ['ase110-200','ase1(10-200300-400)', 'ase1(10-400-10)']
cases_dict['regex_partial_deletion_removed'] = ['ase\u0394110-200','ase1\u0394(10-200300-400)']
cases_dict['regex_delins'] = ['ase1-P114-PVPAL', 'ase1-P114A,Q117A,', 'ase1-,P114A,Q117A', 'ase1-P114AQ117A']
cases_dict['regex_delins_and_partial_deletion'] = ['ase1(10-200)P224A,Q337A,L400*','ase1-,P224A,Q337A,L400*', 'ase1(10-200)-P224AQ337A,L400*']
cases_dict['regex_CTD'] = [ 'ase1-CTD-(r1-r12)',
                            'ase1-CTD-Y1F(r1-r29-r2)',
                            'ase1-S2A,N494D-CTD-Y1FS5A(r11-r29),\u0394(r11-r29)',
                            'ase1-CTD-S5A(r1-r12)\u0394(r13-r29)',
                            'ase1-CTD-']

# Switch case on the keys of regex_dict
for key in cases_dict:
    # Switch case on the values of cases_dict
    for value in cases_dict[key]:
        # Test if the regex matches the value
        match = re.match('ase1' + regex_dict[key] + '$', value)
        if match:
            print(match.group())
        assert re.fullmatch('ase1' + regex_dict[key] + '$', value) is None, f'{value} matches {regex_dict[key]}'



print('All tests passed! :)')