Spectrum feature generator #178
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…into spectrum-feature-generator
…into spectrum-feature-generator
…into spectrum-feature-generator
…trum-feature-generator
pull main in spectrum-feature-generator
…pectrum-feature-generator
…mics/ms2rescore into spectrum-feature-generator
…mics/ms2rescore into spectrum-feature-generator
paretje
reviewed
Jan 6, 2025
| (psm_list["qvalue"] <= 0.01) | ||
| & (psm_list["rank"] <= max_rank) | ||
| & (~psm_list["is_decoy"]) | ||
| & ([metadata.get("original_psm", True) for metadata in psm_list["metadata"]]) |
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This seems like it might be quite inefficient, however I'm not sure if it can be improved significantly, given that original_psm is in the metadata dict. Maybe keeping it a series instead of a list might be better. Or adding it to the dataframe.
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| if original_matched_ions_pct > matched_ions[i]: | ||
| keep[i] = False | ||
| else: | ||
| keep[i] = True |
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Suggested change
| if original_matched_ions_pct > matched_ions[i]: | |
| keep[i] = False | |
| else: | |
| keep[i] = True | |
| keep[i] = original_matched_ions_pct <= matched_ions[i] |
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| if "matched_ions_pct" in psm_list[0].rescoring_features: | ||
| matched_ions = [psm.rescoring_features["matched_ions_pct"] for psm in psm_list] | ||
| else: | ||
| return psm_list |
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Suggested change
| if "matched_ions_pct" in psm_list[0].rescoring_features: | |
| matched_ions = [psm.rescoring_features["matched_ions_pct"] for psm in psm_list] | |
| else: | |
| return psm_list | |
| if "matched_ions_pct" not in psm_list[0].rescoring_features: | |
| return psm_list | |
| else: | |
| matched_ions = [psm.rescoring_features["matched_ions_pct"] for psm in psm_list] |
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| class MS2FeatureGenerator(FeatureGeneratorBase): | ||
| """DeepLC retention time-based feature generator.""" |
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I guess this docstring should be updated?
| } | ||
| except AttributeError: | ||
| raise ParseSpectrumError( | ||
| "Could not parse spectrum IDs using ´spectrum_id_pattern´. Please make sure that there is a capturing in the pattern." |
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Do you mean a capture group with "a capturing"?
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| for peak in annotated_spectrum: | ||
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| for fragment in peak.annotation: | ||
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| ion_type = infer_fragment_identity(fragment) | ||
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| if ion_type == 'b': | ||
| b_intensities.append(peak.intensity) | ||
| if ion_type == 'y': | ||
| y_intensities.append(peak.intensity) | ||
| return b_intensities, y_intensities |
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Suggested change
| for peak in annotated_spectrum: | |
| for fragment in peak.annotation: | |
| ion_type = infer_fragment_identity(fragment) | |
| if ion_type == 'b': | |
| b_intensities.append(peak.intensity) | |
| if ion_type == 'y': | |
| y_intensities.append(peak.intensity) | |
| return b_intensities, y_intensities | |
| for peak in annotated_spectrum: | |
| for fragment in peak.annotation: | |
| ion_type = infer_fragment_identity(fragment) | |
| if ion_type == 'b': | |
| b_intensities.append(peak.intensity) | |
| elif ion_type == 'y': | |
| y_intensities.append(peak.intensity) | |
| return b_intensities, y_intensities |
| return annotated_spectrum.spectrum | ||
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| def factorial(n): |
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Any reason to use a custom function instead of math.factorial?
| if spectrum_filepath.suffix.lower() == ".mzml": | ||
| return mzml.PreIndexedMzML(str(spectrum_filepath)) | ||
| elif spectrum_filepath.suffix.lower() == ".mgf": | ||
| return mgf.IndexedMGF(str(spectrum_filepath)) |
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It might be better to avoid failing silently and add an else and raise an e.g. NotImplementedError or ValueError.
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