Refactor readers x #252
Refactor readers x #252
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| @@ -262,3 +265,4 @@ sage: | |||
| 'peptide_fdr': 'peptide_q' | |||
| 'protein_fdr': 'protein_q' | |||
| 'decoy': 'is_decoy' | |||
| modification_mapping_type: 'maxquant' | |||
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I'm not sure if this has an effect. sage uses a different mapping method to my knowledge.
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good catch .. this works because in sageReader, _translate_modifications() is overwritten .. will change the yaml
| @@ -13,13 +13,8 @@ alphapept: | |||
| 'raw_name': 'raw_name' #parse from `ms_data.hdf`` file | |||
| 'fdr': 'q_value' | |||
| 'decoy': 'decoy' | |||
| modification_mapping: | |||
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I think we shall show here that if search engines use unimod_id
| @@ -119,8 +124,7 @@ pfind: | |||
| 'uniprot_ids': 'Proteins' | |||
| 'fdr': 'Q-value' | |||
| 'decoy': ['Target/Decoy', 'Targe/Decoy'] | |||
| modification_mapping: | |||
| '': '' | |||
| modification_mapping_type: 'maxquant' | |||
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pFind does not use MaxQuant-like PTM format? Did this pass the pFind tests?
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good catch .. this works because in pFindReader, _translate_modifications() is overwritten .. will change the yaml
move more responsibility to psm_reader.yaml
also, changed the structure of
psm_reader.yaml: all modification_mappings are now gathered under one key and referenced by readers.. let me know what you think!