Added peak level annotations support #83
Added peak level annotations support #83bhavyak7-lab wants to merge 13 commits intowfondrie:mainfrom
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depthcharge/data/parsers.py
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| raise ValueError("Invalid precursor charge.") | ||
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| class AsfParser(BaseParser): |
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Can ASF parser extend the MGF parser instead? Might reduce a little bit of redundancy.
depthcharge/data/parsers.py
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| if "=" in line: | ||
| key, value = line.split("=", 1) | ||
| if key == "CHARGE": | ||
| if len(value) == 2: |
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What is this length = 2 check for?
| if len(value) == 2: | ||
| value = value[0] | ||
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| if key == "PEPMASS": |
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We do not always expect a precursor intensity to also be provided (in fact unless you do a special feature extraction step DIA data we will never have it). We should handle not having it.
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This case would be handled by the final line: spectrum["params"][key.lower()] = [value]
| if key == "SEQ": | ||
| spectrum["params"][key.lower()] = value | ||
| continue | ||
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Can we add support for skipping spectra where key parameters are missing / of the incorrect format, and warn the users that these spectra were skipped?
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If the charge is outside of the range, the iter_batches method throws an error. Should I also throw an error here?
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| def parse_spectrum(self, spectrum: dict) -> MassSpectrum: |
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This function is 99% the same as the one for MGF parser. If we extend that class instead, this can just call super() and then set the peak_annotations=spectrum["peak_annotations"] on the result.
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The failing TDF tests are due to a file-reading issue with MACOS as the tests pass on Linux. |
2 participants
Changes made:
Users can extract peak level annotations by creating a custom field to extract them, and they are stored in the spectrum dictionary