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* getting there * working in the pipeline and the API * changed convert_ctd api endpoint response type
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| import re | ||
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| aa = 'GPAVLIMCFYWHKRQNEDST' | ||
| aa = aa + aa.lower() | ||
| aa = f'[{aa}]' | ||
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| ctd_repetition_regex = r'\(r\d+-r\d+(?:-\d+)?\)' | ||
| ctd_repetition_regex_with_groups = r'\(r(\d+)-r(\d+)(?:-(\d+))?\)' | ||
| ctd_mutation_regex = f'{aa}\d+{aa}(?:{ctd_repetition_regex})?' | ||
| ctd_deletion_regex = f'(?:delta|\u0394|∆)(?:{ctd_repetition_regex})?' | ||
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| # This dictionary has keys that are the systematic IDs of the genes that have CTDs, | ||
| # the value is a dictionary with: | ||
| # - positions: a dictionary with keys that are the residues of the canonical repeat | ||
| # e.g. YSPTSPS for SPBC28F2.12, and the value is the repeats in which the residue is | ||
| # present, zero-based index. | ||
| # - shifts: a tuple of two integers the first value is the position in the protein where | ||
| # an aminoacid is missing (-1) or inserted (+1) with respect to the canonical repeat. | ||
| # There is only one in rpb1, but a list of tuples could be used if more are needed. | ||
| # - start: the position of the first residue of the CTD in the protein (zero-based index) | ||
| # - length: the length of the CTD | ||
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| rpb1_dictionary = { | ||
| 'positions': { | ||
| 'Y1': range(29), | ||
| 'S2': [1, 2] + list(range(4, 29)), | ||
| 'P3': [1, ] + list(range(3, 8)) + list(range(9, 29)), | ||
| 'T4': [0, 2] + list(range(4, 29)), | ||
| 'S5': range(29), | ||
| 'P6': range(29), | ||
| 'S7': [0, 3] + list(range(4, 29)), | ||
| }, | ||
| 'shift': (1566, -1), | ||
| 'start': 1550, | ||
| 'length': 202, | ||
| 'nb_repeats': 29, | ||
| } | ||
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| def apply_shift(match: re.match, shift: tuple[int, int]): | ||
| num_str = match.group() | ||
| num = int(num_str) | ||
| # If the number is smaller than the position of the missing aminoacid, | ||
| # return the number | ||
| if num <= shift[0]: | ||
| return num_str | ||
| # If the number is bigger than the position of the missing aminoacid, | ||
| # return the number plus the shift | ||
| return str(shift[1] + num) | ||
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| def ctd_further_check(g, gg): | ||
| return gg['CDS'].qualifiers['systematic_id'][0] in ['SPBC28F2.12'] | ||
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| def ctd_convert_to_normal_variant(ctd_substring: str): | ||
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| mutations = re.findall(ctd_mutation_regex, ctd_substring) | ||
| deletions= re.findall(ctd_deletion_regex, ctd_substring) | ||
| starting_position = rpb1_dictionary['start'] | ||
| repeat_length = len(rpb1_dictionary['positions']) | ||
| out_list = [] | ||
| deleted_repeats = list() | ||
| for deletion in deletions: | ||
| # Entire deletion, always correct, and takes over everything else | ||
| if '(' not in deletion: | ||
| return '{}-{}'.format(rpb1_dictionary['start'] + 1, rpb1_dictionary['start'] + rpb1_dictionary['length']) | ||
| # Deletion with repeat number | ||
| match = re.search(ctd_repetition_regex_with_groups, deletion) | ||
| start, stop, step = match.groups() | ||
| step = int(step) if step is not None else 1 | ||
| start, stop = int(start), int(stop) | ||
| deleted_ranges = list() | ||
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| for repeat_number in range(start, stop + 1, step): | ||
| deleted_repeats.append(repeat_number) | ||
| repeat_start = (repeat_number - 1) * repeat_length + starting_position + 1 | ||
| repeat_end = repeat_start + repeat_length - 1 | ||
| deleted_ranges.append((repeat_start, repeat_end)) | ||
| if step == 1: | ||
| out_list.append('{}-{}'.format(deleted_ranges[0][0], deleted_ranges[-1][1])) | ||
| else: | ||
| out_list.append(','.join(['{}-{}'.format(*x) for x in deleted_ranges])) | ||
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| for mutation in mutations: | ||
| original_residue, index_in_repeat, replaced_by = re.search(r'([A-Za-z])(\d+)([A-Za-z])', mutation).groups() | ||
| index_in_repeat = int(index_in_repeat) | ||
| repeats_where_residue_is_present = rpb1_dictionary['positions'][mutation[:2]] | ||
| match = re.search(ctd_repetition_regex_with_groups, mutation) | ||
| if match is None: | ||
| start, stop, step = 1, rpb1_dictionary['nb_repeats'], 1 | ||
| else: | ||
| start, stop, step = match.groups() | ||
| step = int(step) if step is not None else 1 | ||
| start, stop = int(start), int(stop) | ||
| for repeat_number in range(start, stop + 1, step): | ||
| if repeat_number in deleted_repeats: | ||
| continue | ||
| if repeat_number - 1 not in repeats_where_residue_is_present: | ||
| continue | ||
| mutated_position = index_in_repeat + (repeat_number - 1) * repeat_length + starting_position | ||
| out_list.append('{}{}{}'.format(original_residue, mutated_position, replaced_by)) | ||
| out_str = ','.join(out_list) | ||
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| return re.sub(r'(\d+)', lambda x: apply_shift(x, rpb1_dictionary['shift']), out_str) | ||
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| def ctd_check_sequence(ctd_substring: str): | ||
| sequence_errors = [] | ||
| mutations = re.findall(ctd_mutation_regex, ctd_substring) | ||
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| for mutation in mutations: | ||
| if mutation[:2] not in rpb1_dictionary['positions']: | ||
| sequence_errors.append('CTD-' + mutation[:2]) | ||
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| match = re.search(ctd_repetition_regex_with_groups, ctd_substring) | ||
| start, stop, step = match.groups() | ||
| if int(stop) > rpb1_dictionary['nb_repeats']: | ||
| sequence_errors.append('CTD-r' + stop) | ||
| if int(start) > rpb1_dictionary['nb_repeats']: | ||
| sequence_errors.append('CTD-r' + start) | ||
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| return '/'.join(sequence_errors) | ||
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| def ctd_format_for_transvar(capture_groups: list[str], gene: dict) -> list[str]: | ||
| ctd_substring = capture_groups[0] | ||
| result = list() | ||
| for ele in ctd_convert_to_normal_variant(ctd_substring).split(','): | ||
| if '-' in ele: | ||
| result.append('p.{}_{}del'.format(*ele.split('-'))) | ||
| else: | ||
| result.append('p.{}'.format(ele)) | ||
| return result | ||
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| def ctd_apply_syntax(ctd_substring: str): | ||
| ctd_bits = re.findall(f'({ctd_mutation_regex}|{ctd_deletion_regex})', ctd_substring) | ||
| return 'CTD-' + ','.join(ctd_bits) |
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