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Flexible format for scan titles #369

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Flexible format for scan titles #369

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2738492
Use different scan titles in test mzML
bittremieux Aug 22, 2024
cdfc98d
Update tests for matching scan id
bittremieux Aug 22, 2024
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10 changes: 8 additions & 2 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,13 @@ def _create_mzml(peptides, mzml_file, random_state=42):
)
with writer.run(id=1, instrument_configuration="ic"):
with writer.spectrum_list(len(peptides)):
for scan_nr, peptide in zip([17, 111], peptides):
for scan_id, peptide in zip(
[
"scan=17",
"merged=11 frame=12 scanStart=763 scanEnd=787",
],
peptides,
):
charge = rng.choice([2, 3])

precursor = writer.precursor_builder()
Expand All @@ -193,7 +199,7 @@ def _create_mzml(peptides, mzml_file, random_state=42):
writer.write_spectrum(
mzs,
intensities,
id=f"scan={scan_nr}",
id=scan_id,
centroided=True,
params=[{"ms level": 2}],
precursor_information=precursor,
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5 changes: 4 additions & 1 deletion tests/test_integration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,10 @@ def test_train_and_run(
assert psms.loc[3, "sequence"] == "LESLLEK"
assert psms.loc[3, "spectra_ref"] == "ms_run[2]:scan=17"
assert psms.loc[4, "sequence"] == "PEPTLDEK"
assert psms.loc[4, "spectra_ref"] == "ms_run[2]:scan=111"
assert (
psms.loc[4, "spectra_ref"]
== "ms_run[2]:merged=11 frame=12 scanStart=763 scanEnd=787"
)

# Finally, try evaluating:
output_filename = tmp_path / "test-eval.mztab"
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14 changes: 7 additions & 7 deletions tests/unit_tests/test_unit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -864,23 +864,23 @@ def test_spectrum_id_mgf(mgf_small, tmp_path):


def test_spectrum_id_mzml(mzml_small, tmp_path):
"""Test that spectra from mzML files are specified by their scan number."""
"""Test that spectra from mzML files are specified by their scan id."""
mzml_small2 = tmp_path / "mzml_small2.mzml"
shutil.copy(mzml_small, mzml_small2)

index = SpectrumIndex(
tmp_path / "index.hdf5", [mzml_small, mzml_small2], overwrite=True
)
dataset = SpectrumDataset(index)
for i, (filename, scan_nr) in enumerate(
for i, (filename, scan_id) in enumerate(
[
(mzml_small, 17),
(mzml_small, 111),
(mzml_small2, 17),
(mzml_small2, 111),
(mzml_small, "scan=17"),
(mzml_small, "merged=11 frame=12 scanStart=763 scanEnd=787"),
(mzml_small2, "scan=17"),
(mzml_small2, "merged=11 frame=12 scanStart=763 scanEnd=787"),
]
):
spectrum_id = str(filename), f"scan={scan_nr}"
spectrum_id = str(filename), scan_id
assert dataset.get_spectrum_id(i) == spectrum_id


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