Useful utilities for helping in parsing GenBank files.
- class Bio.GenBank.utils.FeatureValueCleaner(to_process=keys_to_process)¶
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:
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']¶
- __init__(self, to_process=keys_to_process)¶
Initialize with the keys we should deal with.
Return a string representation of the class.
- 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.