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mo-sameh
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mschwoer
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| """Convert precursor and fragment frames to a SWATH transition list. | ||
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| The dataframe-in form of :func:`speclib_to_single_df`, so that one batch of | ||
| The dataframe-in form of :func:`speclib_to_swath_df`, so that one batch of |
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(I know this is not part of this PR)
The naming SWATH here is a bit confusing. I would maybe call it just "spectral library" and do a full rename in a separate PR.
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I had a hard time naming this too. I don't think plain "spectral library" works though because the DIA-NN parquet export is also a spectral library, so the name wouldn't tell the two apart.
`Flags` marked the base peak by grouping on `Precursor.Id`, which is not unique: `SpecLibBase.append` produces libraries holding the same precursor twice, and those shared a single flag between them.
`fragment_table` built a frame of lists and exploded it, and `explode` yields object columns. The DIA-NN export casts them against its schema; the SWATH one does not, so it returned `FragmentMz`, `RelativeIntensity`, `FragmentCharge` and `FragmentNumber` as objects of boxed scalars -- and the charge as strings, since it is sliced out of a fragment column name and was never converted. Concatenate the columns instead of exploding them: m/z and intensity keep the dtype of the frame they came from, the charge and series number become int64. That also removes the all-NaN row the explode needed dropped. `translate_to_tsv` never checked its writer process. `multiprocessing=True` is the default, and that process dies before writing anything if the calling script has no `if __name__ == "__main__":` guard, so the export printed its success message and returned over a 0-byte tsv. Raise on a non-zero exit code. The written tsv and parquet are byte-identical; only the in-memory frames change, and only in dtype -- plus `FragmentCharge` "1" -> 1. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Goal
Fix the remaining defects the characterization tests exposed, now that the structure makes them one-line changes, and give the exports names that say what they produce.
What's here
rt_norm_predis accepted as a retention time. peptdeep writes it alongsidert_pred, so a library whosert_predwas dropped was rejected outright.Flagsmarks one base peak per precursor row. It grouped onPrecursor.Id, which is not unique —SpecLibBase.appendproduces libraries holding the same precursor twice, and those shared a single flag. Two appended libraries: 8 flags for 16 precursor rows, now 16.object, andFragmentChargeheld strings, so arithmetic on it concatenated. The written tsv and parquet are byte-identical; only the in-memory frames change.translate_to_tsvnotices a dead writer.multiprocessing=Trueis the default, and that process dies before writing anything if the calling script has noif __name__ == "__main__":guard — the norm on macOS and Windows. The export printed its success message and returned over a 0-byte file.speclib_to_single_dfis nowspeclib_to_swath_df. The good name already existed as a wrapper that has been missing itsreturnsince the module arrived from AlphaPeptDeep in 2022, so it only ever returnedNone. The real function takes the name; the old one stays as a deprecated alias. Nothing breaks — the wrapper's arguments are a subset, under the same names and defaults.The module now reads
speclib_to_*_dfto build a frame,translate_to_*to write a file.