FEAT allow custom fragment types #136
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mschwoer
approved these changes
May 13, 2024
| @@ -257,11 +285,18 @@ def __init__( | |||
| self.mp_process_num = mp_process_num | |||
| self.checkpoint_folder_path = checkpoint_folder_path | |||
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| self.fragment_types = fragment_types | |||
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could those variables be private?
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Yep, All of them 👍🏻
| @@ -199,6 +200,12 @@ def _parse_modifications(mod_str: str) -> typing.List[str]: | |||
| checkpoint_folder_path=self.config["library_prediction"][ | |||
| "checkpoint_folder_path" | |||
| ], | |||
| fragment_types=self.config["library_prediction"][ | |||
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introducing lib_pred_config = self.config["library_prediction"] here might be easier on the eye
| fragment_types: 'b;y' | ||
| # maximum charge state for predicted fragments | ||
| max_fragment_charge: 2 | ||
| instrument: Lumos |
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just out of interest: where could the user find a list of supported instruments?
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That's a bit of a challenge and also applies to enzymes, modifications, instruments. They are constants in peptdeep. @vbrennsteiner and I briefly discussed a nice GUI solution for this.
jalew188
reviewed
May 13, 2024
jalew188
approved these changes
May 13, 2024
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This PR allows to set other fragment types and charges than
b,yfor PeptDeep library prediction.For example it allows to set
b_modloss;y_modlossfor phospho search.