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[FIX](all): Accept lists in different formats on input properties.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,31 +1,115 @@ | ||
| """ Common functions for package biobb_pmx.pmx """ | ||
| """Common functions for package biobb_pmx.pmx""" | ||
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| import re | ||
| from typing import Union, Iterable, Mapping | ||
| from typing import Iterable, Mapping, Optional, Union | ||
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| MUTATION_DICT = { | ||
| "ALA": "A", | ||
| "ARG": "R", | ||
| "ASN": "N", | ||
| "ASP": "D", | ||
| "ASPH": "B", | ||
| "ASPP": "B", | ||
| "ASH": "B", | ||
| "CYS": "C", | ||
| "CYS2": "C", | ||
| "CYN": "C", | ||
| "CYX": "CX", | ||
| "CYM": "CM", | ||
| "CYSH": "C", | ||
| "GLU": "E", | ||
| "GLUH": "J", | ||
| "GLUP": "J", | ||
| "GLH": "J", | ||
| "GLN": "Q", | ||
| "GLY": "G", | ||
| "HIS": "H", | ||
| "HIE": "X", | ||
| "HISE": "X", | ||
| "HSE": "X", | ||
| "HIP": "Z", | ||
| "HSP": "Z", | ||
| "HISH": "Z", | ||
| "HID": "H", | ||
| "HSD": "H", | ||
| "ILE": "I", | ||
| "LEU": "L", | ||
| "LYS": "K", | ||
| "LYSH": "K", | ||
| "LYP": "K", | ||
| "LYN": "O", | ||
| "LSN": "O", | ||
| "MET": "M", | ||
| "PHE": "F", | ||
| "PRO": "P", | ||
| "SER": "S", | ||
| "SP1": "SP1", | ||
| "SP2": "SP2", | ||
| "THR": "T", | ||
| "TRP": "W", | ||
| "TYR": "Y", | ||
| "VAL": "V", | ||
| "A": "A", | ||
| "T": "T", | ||
| "C": "C", | ||
| "G": "G", | ||
| "U": "U", | ||
| } | ||
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| MUTATION_DICT = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'ASPH': 'B', 'ASPP': 'B', 'ASH': 'B', 'CYS': 'C', 'CYS2': 'C', 'CYN': 'C', 'CYX': 'CX', 'CYM': 'CM', 'CYSH': 'C', 'GLU': 'E', 'GLUH': 'J', 'GLUP': 'J', 'GLH': 'J', 'GLN': 'Q', 'GLY': 'G', 'HIS': 'H', 'HIE': 'X', 'HISE': 'X', 'HSE': 'X', 'HIP': 'Z', 'HSP': 'Z', 'HISH': 'Z', 'HID': 'H', 'HSD': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K', 'LYSH': 'K', 'LYP': 'K', 'LYN': 'O', 'LSN': 'O', 'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'SER': 'S', 'SP1': 'SP1', 'SP2': 'SP2', 'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V', 'A': 'A', 'T': 'T', 'C': 'C', 'G': 'G', 'U': 'U'} | ||
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| def create_mutations_file(input_mutations_path: str, mutation_list: Union[str, Iterable[str]], mutation_dict: Mapping) -> str: | ||
| def create_mutations_file( | ||
| input_mutations_path: str, | ||
| mutation_list: Union[str, Iterable[str]], | ||
| mutation_dict: Mapping, | ||
| ) -> str: | ||
| try: | ||
| # Check if self.mutation_list is a string | ||
| mutation_list = mutation_list.replace(" ", "").split(',') # type: ignore | ||
| mutation_list = mutation_list.replace(" ", "").split(",") # type: ignore | ||
| except AttributeError: | ||
| pass | ||
| pattern = re.compile(r"(?P<chain>[a-zA-Z])*:?(?P<resnum>\d+)(?P<mt>[a-zA-Z0-9]+)") | ||
| with open(input_mutations_path, 'w') as mut_file: | ||
| with open(input_mutations_path, "w") as mut_file: | ||
| for mut in mutation_list: | ||
| match = pattern.match(mut.strip()) | ||
| if match: | ||
| mut_groups_dict = match.groupdict() | ||
| if mut_groups_dict.get('chain'): | ||
| mut_file.write(mut_groups_dict.get('chain', '') + ' ') | ||
| mut_file.write(mut_groups_dict.get('resnum', '') + ' ') | ||
| if not mut_groups_dict.get('mt', '').upper() in mutation_dict.keys(): | ||
| if mut_groups_dict.get("chain"): | ||
| mut_file.write(mut_groups_dict.get("chain", "") + " ") | ||
| mut_file.write(mut_groups_dict.get("resnum", "") + " ") | ||
| if mut_groups_dict.get("mt", "").upper() not in mutation_dict.keys(): | ||
| raise TypeError( | ||
| f"{mut_groups_dict.get('mt','').upper()} is not a valid AA code or NA code. Possible values are {mutation_dict.keys()}") | ||
| mut_file.write(mutation_dict[mut_groups_dict.get('mt', '').upper()]) | ||
| mut_file.write('\n') | ||
| f"{mut_groups_dict.get('mt','').upper()} is not a valid AA code or NA code. Possible values are {mutation_dict.keys()}" | ||
| ) | ||
| mut_file.write(mutation_dict[mut_groups_dict.get("mt", "").upper()]) | ||
| mut_file.write("\n") | ||
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| return input_mutations_path | ||
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| # TODO: Move this function to biobb_common.tools.file_utils | ||
| def _from_string_to_list(input_data: Optional[Union[str, list[str]]]) -> list[str]: | ||
| """ | ||
| Converts a string to a list, splitting by commas or spaces. If the input is already a list, returns it as is. | ||
| Returns an empty list if input_data is None. | ||
| Parameters: | ||
| input_data (str, list, or None): The string, list, or None value to convert. | ||
| Returns: | ||
| list: A list of string elements or an empty list if input_data is None. | ||
| """ | ||
| if input_data is None: | ||
| return [] | ||
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| if isinstance(input_data, list): | ||
| # If input is already a list, return it | ||
| return input_data | ||
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| # If input is a string, determine the delimiter based on presence of commas | ||
| delimiter = "," if "," in input_data else " " | ||
| items = input_data.split(delimiter) | ||
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| # Remove whitespace from each item and ignore empty strings | ||
| processed_items = [item.strip() for item in items if item.strip()] | ||
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| return processed_items |
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