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Various minor improvements #137

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merged 1 commit into from
Mar 28, 2024
Merged

Various minor improvements #137

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5 changes: 5 additions & 0 deletions ms2rescore/feature_generators/ms2pip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ def __init__(
ms2_tolerance: float = 0.02,
spectrum_path: Optional[str] = None,
spectrum_id_pattern: str = "(.*)",
model_dir: Optional[str] = None,
processes: 1,
**kwargs,
) -> None:
Expand All @@ -71,6 +72,8 @@ def __init__(
spectrum_id_pattern : str, optional
Regular expression pattern to extract spectrum ID from spectrum file. Defaults to
:py:const:`.*`.
model_dir
Directory containing MS²PIP models. Defaults to :py:const:`None` (use MS²PIP default).
processes : int, optional
Number of processes to use. Defaults to 1.

Expand All @@ -85,6 +88,7 @@ def __init__(
self.ms2_tolerance = ms2_tolerance
self.spectrum_path = spectrum_path
self.spectrum_id_pattern = spectrum_id_pattern
self.model_dir = model_dir
self.processes = processes

@property
Expand Down Expand Up @@ -194,6 +198,7 @@ def add_features(self, psm_list: PSMList) -> None:
model=self.model,
ms2_tolerance=self.ms2_tolerance,
compute_correlations=False,
model_dir=self.model_dir,
processes=self.processes,
)
except NoMatchingSpectraFound as e:
Expand Down
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