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PSMList: Use np.fromiter when using a string as accessor (e.g. psm_list["peptidoform"]) #102

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merged 3 commits into from
Nov 19, 2024
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PSMList: Use np.fromiter when using a string as accessor (e.g. psm_list["peptidoform"]) #102

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7205421
Fix issue where an array of peptidoforms is coerced into a 2D array o…
RalfG Oct 23, 2024
bb5073f
Update tests
RalfG Oct 23, 2024
0d47b14
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RalfG Oct 23, 2024
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7 changes: 1 addition & 6 deletions psm_utils/psm_list.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,12 +98,7 @@ def __getitem__(self, item) -> PSM | list[PSM]:
return PSMList(psm_list=self.psm_list[item])
elif isinstance(item, str):
# Return PSM property as array across full PSMList
try:
# Let NumPy coerce dtype (e.g., multidimensional arrays)
return np.array([psm[item] for psm in self.psm_list])
except ValueError:
# If dtype is not consistent, force dtype to be object
return np.array([psm[item] for psm in self.psm_list], dtype=object)
return np.fromiter([psm[item] for psm in self.psm_list], dtype=object, count=len(self))
elif _is_iterable_of_bools(item):
# Return new PSMList with items that were True
return PSMList(psm_list=[self.psm_list[i] for i in np.flatnonzero(item)])
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4 changes: 2 additions & 2 deletions tests/test_psm_list.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import numpy as np
import pytest

from psm_utils import Peptidoform, PSM, PSMList
from psm_utils import PSM, Peptidoform, PSMList

sample_psm_list = [
PSM(peptidoform="ACDK", spectrum_id=1, score=140.2),
Expand Down Expand Up @@ -42,7 +42,7 @@ def test___get_item__(self):
# Multiple PSM properties as 2D array
np.testing.assert_equal(
psm_list[["spectrum_id", "score"]],
np.array([["1", 140.2], ["2", 132.9], ["3", 55.7]]),
np.array([["1", 140.2], ["2", 132.9], ["3", 55.7]], dtype=object),
)

# Index by multiple indices
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