| |
| |
| |
| |
|
|
| """Useful utilities for helping in parsing GenBank files.""" |
|
|
|
|
| class FeatureValueCleaner: |
| r"""Provide specialized capabilities for cleaning up values in features. |
| |
| This class is designed to provide a mechanism to clean up and process |
| values in the key/value pairs of GenBank features. This is useful |
| because in cases like:: |
| |
| /translation="MED |
| YDPWNLRFQSKYKSRDA" |
| |
| you'll otherwise end up with white space in it. |
| |
| This cleaning needs to be done on a case by case basis since it is |
| impossible to interpret whether you should be concatenating everything |
| (as in translations), or combining things with spaces (as might be |
| the case with /notes). |
| |
| >>> cleaner = FeatureValueCleaner(["translation"]) |
| >>> cleaner |
| FeatureValueCleaner(['translation']) |
| >>> cleaner.clean_value("translation", "MED\nYDPWNLRFQSKYKSRDA") |
| 'MEDYDPWNLRFQSKYKSRDA' |
| """ |
|
|
| keys_to_process = ["translation"] |
|
|
| def __init__(self, to_process=keys_to_process): |
| """Initialize with the keys we should deal with.""" |
| self._to_process = to_process |
|
|
| def __repr__(self): |
| """Return a string representation of the class.""" |
| return f"{self.__class__.__name__}({self._to_process!r})" |
|
|
| def clean_value(self, key_name, value): |
| """Clean the specified value and return it. |
| |
| If the value is not specified to be dealt with, the original value |
| will be returned. |
| """ |
| if key_name in self._to_process: |
| try: |
| cleaner = getattr(self, f"_clean_{key_name}") |
| except AttributeError: |
| raise AssertionError(f"No function to clean key: {key_name}") from None |
| value = cleaner(value) |
| return value |
|
|
| def _clean_translation(self, value): |
| """Concatenate a translation value to one long protein string (PRIVATE).""" |
| translation_parts = value.split() |
| return "".join(translation_parts) |
|
|
|
|
| if __name__ == "__main__": |
| from Bio._utils import run_doctest |
|
|
| run_doctest() |
|
|
