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Merge pull request #247 from MannLabs/refactor_readers_V
Refactor readers v
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,170 @@ | ||
| """Module to handle modification mappings for different search engines.""" | ||
|
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| import copy | ||
| from collections import defaultdict | ||
| from typing import Dict, Optional | ||
|
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| from alphabase.psm_reader.utils import MOD_TO_UNIMOD_DICT, get_extended_modifications | ||
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| class ModificationMapper: | ||
| """Class to handle modification mappings for different search engines.""" | ||
|
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| def __init__( | ||
| self, | ||
| custom_modification_mapping: Optional[Dict[str, str]], | ||
| reader_yaml: Dict, | ||
| modification_type: Optional[str], | ||
| *, | ||
| add_unimod_to_mod_mapping: bool, | ||
| ): | ||
| """Initialize the ModificationMapper. | ||
| Parameters | ||
| ---------- | ||
| custom_modification_mapping: | ||
| A custom mapping or a string referencing one of the mappings in the reader_yaml | ||
| The key of dict is a modification name in AlphaBase format; | ||
| the value could be a str or a list, see below | ||
| ``` | ||
| add_modification_mapping({ | ||
| 'Dimethyl@K': ['K(Dimethyl)'], # list | ||
| 'Dimethyl@Any_N-term': '_(Dimethyl)', # str | ||
| }) | ||
| reader_yaml: | ||
| the yaml (read from file) containing the modification mappings | ||
| modification_type: | ||
| the type of modification mapping ("maxquant" or "alphapept") | ||
| add_unimod_to_mod_mapping: | ||
| whether unimod modifications should be added to the mapping | ||
| """ | ||
| self._psm_reader_yaml = reader_yaml | ||
| self._add_unimod_to_mod_mapping = add_unimod_to_mod_mapping | ||
| self._modification_type = modification_type | ||
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| self.modification_mapping = None | ||
| self.rev_mod_mapping = None | ||
| self.set_modification_mapping() | ||
| self.add_modification_mapping(custom_modification_mapping) | ||
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| def add_modification_mapping(self, custom_modification_mapping: dict) -> None: | ||
| """Append additional modification mappings for the search engine. | ||
| Also creates a reverse mapping from the modification format used by the search engine to the AlphaBase format. | ||
| Parameters | ||
| ---------- | ||
| custom_modification_mapping : dict | ||
| The key of dict is a modification name in AlphaBase format; | ||
| the value could be a str or a list, see below | ||
| ``` | ||
| add_modification_mapping({ | ||
| 'Dimethyl@K': ['K(Dimethyl)'], # list | ||
| 'Dimethyl@Any_N-term': '_(Dimethyl)', # str | ||
| }) | ||
| ``` | ||
| """ | ||
| if not isinstance(custom_modification_mapping, dict): | ||
| return | ||
|
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| new_modification_mapping = defaultdict(list) | ||
| for key, val in list(custom_modification_mapping.items()): | ||
| if isinstance(val, str): | ||
| new_modification_mapping[key].append(val) | ||
| else: | ||
| new_modification_mapping[key].extend(val) | ||
|
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| if new_modification_mapping: | ||
| self.set_modification_mapping( | ||
| self.modification_mapping | new_modification_mapping | ||
| ) | ||
|
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| def set_modification_mapping( | ||
| self, modification_mapping: Optional[Dict] = None | ||
| ) -> None: | ||
| """Set the modification mapping for the search engine. | ||
| Also creates a reverse mapping from the modification format used by the search engine to the AlphaBase format. | ||
| Parameters | ||
| ---------- | ||
| modification_mapping: | ||
| If dictionary: the current modification_mapping will be overwritten by this. | ||
| If str: the parameter will be interpreted as a reader type, and the modification_mapping is read from the | ||
| "modification_mapping" section of the psm_reader_yaml | ||
| """ | ||
| if modification_mapping is None: | ||
| self._init_modification_mapping() | ||
| elif isinstance( | ||
| modification_mapping, str | ||
| ): # TODO: remove this overloading of the parameter by introducing yaml key "modification_mapping_type" | ||
| if modification_mapping in self._psm_reader_yaml: | ||
| self.modification_mapping = self._psm_reader_yaml[modification_mapping][ | ||
| "modification_mapping" | ||
| ] | ||
| else: | ||
| raise ValueError( | ||
| f"Unknown modification mapping: {modification_mapping}" | ||
| ) | ||
| else: | ||
| self.modification_mapping = copy.deepcopy(modification_mapping) | ||
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| self._str_mods_to_lists() | ||
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| if self._add_unimod_to_mod_mapping: | ||
| self._add_all_unimod() | ||
| self._extend_mod_brackets() | ||
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| self.rev_mod_mapping = self._get_reversed_mod_mapping() | ||
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| def _init_modification_mapping(self) -> None: | ||
| """Initialize the modification mapping from the psm_reader_yaml or as an empty dictionary.""" | ||
| if self._modification_type is not None: | ||
| self.modification_mapping = self._psm_reader_yaml[self._modification_type][ | ||
| "modification_mapping" | ||
| ] | ||
| else: | ||
| self.modification_mapping = {} | ||
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| def _add_all_unimod(self) -> None: | ||
| """Add all unimod modifications to the modification mapping.""" | ||
| for mod_name, unimod in MOD_TO_UNIMOD_DICT.items(): | ||
| if mod_name in self.modification_mapping: | ||
| self.modification_mapping[mod_name].append(unimod) | ||
| else: | ||
| self.modification_mapping[mod_name] = [unimod] | ||
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| def _extend_mod_brackets(self) -> None: | ||
| """Update modification_mapping to include different bracket types.""" | ||
| for key, mod_list in list(self.modification_mapping.items()): | ||
| self.modification_mapping[key] = get_extended_modifications(mod_list) | ||
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| def _str_mods_to_lists(self) -> None: | ||
| """Convert all single strings to lists containing one item in self.modification_mapping.""" | ||
| for mod, val in list(self.modification_mapping.items()): | ||
| if isinstance(val, str): | ||
| self.modification_mapping[mod] = [val] | ||
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| def _get_reversed_mod_mapping(self) -> Dict[str, str]: | ||
| """Create a reverse mapping from the modification format used by the search engine to the AlphaBase format.""" | ||
| rev_mod_mapping = {} | ||
| for mod_alphabase_format, mod_other_format in self.modification_mapping.items(): | ||
| if isinstance(mod_other_format, (list, tuple)): | ||
| for mod_other_format_ in mod_other_format: | ||
| if ( | ||
| mod_other_format_ in rev_mod_mapping | ||
| and mod_alphabase_format.endswith("Protein_N-term") | ||
| ): | ||
| continue | ||
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| rev_mod_mapping[mod_other_format_] = mod_alphabase_format | ||
| else: | ||
| rev_mod_mapping[mod_other_format] = mod_alphabase_format | ||
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| return rev_mod_mapping |
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