From c6f18c9be3f5f2f5ff41f835832afd30202af924 Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Mon, 8 Apr 2024 16:09:32 +0200
Subject: [PATCH] Add tests for get_ms2_spectra

---
 tests/__init__.py          |  0
 tests/{ => data}/README.md |  0
 tests/test.py              | 38 -------------------
 tests/test_lib.py          | 78 ++++++++++++++++++++++++++++++++++++++
 4 files changed, 78 insertions(+), 38 deletions(-)
 create mode 100644 tests/__init__.py
 rename tests/{ => data}/README.md (100%)
 delete mode 100644 tests/test.py
 create mode 100644 tests/test_lib.py

diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/README.md b/tests/data/README.md
similarity index 100%
rename from tests/README.md
rename to tests/data/README.md
diff --git a/tests/test.py b/tests/test.py
deleted file mode 100644
index 8910a47..0000000
--- a/tests/test.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import pytest
-from ms2rescore_rs import get_precursor_info
-
-
-def test_mgf_precursor_reading():
-    precursor = get_precursor_info("tests/data/test.mgf")["peptide1"]
-    assert precursor.mz == pytest.approx(475.137295, 0.0001)
-    assert precursor.charge == 2
-    assert precursor.intensity == 0
-    assert precursor.rt == pytest.approx(0.853, 0.001)
-    assert precursor.im == 42.42
-
-
-def test_mzml_precursor_reading():
-    precursor = get_precursor_info("tests/data/test.mzML")["index=3"]
-    assert precursor.mz == pytest.approx(1007.8454316970522, 0.0001)
-    assert precursor.charge == 3
-    assert precursor.intensity == 0
-    assert precursor.rt == pytest.approx(40.01385810926034, 0.001)
-    assert precursor.im == 1.2507906843214256
-
-
-def test_bruker_tdf_reading():
-    precursor = get_precursor_info("tests/data/dda_test.d")["2"]
-    assert precursor.mz == pytest.approx(502, 0.0001)
-    assert precursor.charge == 2
-    assert precursor.intensity == 10
-    assert precursor.rt == pytest.approx(0.4, 0.001)
-    assert precursor.im == 1.4989212513484358
-
-
-def test_bruker_minitdf_reading():
-    precursor = get_precursor_info("tests/data/test.ms2")["3"]
-    assert precursor.mz == pytest.approx(502, 0.0001)
-    assert precursor.charge == 2
-    assert precursor.intensity == 0
-    assert precursor.rt == pytest.approx(0.3, 0.001)
-    assert precursor.im == 1.3
diff --git a/tests/test_lib.py b/tests/test_lib.py
new file mode 100644
index 0000000..dea310f
--- /dev/null
+++ b/tests/test_lib.py
@@ -0,0 +1,78 @@
+import pytest
+from ms2rescore_rs import get_precursor_info, get_ms2_spectra
+
+
+def test_get_precursor_info_mgf():
+    precursor = get_precursor_info("tests/data/test.mgf")["peptide1"]
+    assert precursor.mz == pytest.approx(475.137295, 0.0001)
+    assert precursor.charge == 2
+    assert precursor.intensity == 0
+    assert precursor.rt == pytest.approx(0.853, 0.001)
+    assert precursor.im == 42.42
+
+
+def test_get_precursor_info_mzml():
+    precursor = get_precursor_info("tests/data/test.mzML")["index=3"]
+    assert precursor.mz == pytest.approx(1007.8454316970522, 0.0001)
+    assert precursor.charge == 3
+    assert precursor.intensity == 0
+    assert precursor.rt == pytest.approx(40.01385810926034, 0.001)
+    assert precursor.im == 1.2507906843214256
+
+
+def test_get_precursor_info_bruker_tdf():
+    precursor = get_precursor_info("tests/data/dda_test.d")["2"]
+    assert precursor.mz == pytest.approx(502, 0.0001)
+    assert precursor.charge == 2
+    assert precursor.intensity == 10
+    assert precursor.rt == pytest.approx(0.4, 0.001)
+    assert precursor.im == 1.4989212513484358
+
+
+def test_get_precursor_info_bruker_minitdf():
+    precursor = get_precursor_info("tests/data/test.ms2")["3"]
+    assert precursor.mz == pytest.approx(502, 0.0001)
+    assert precursor.charge == 2
+    assert precursor.intensity == 0
+    assert precursor.rt == pytest.approx(0.3, 0.001)
+    assert precursor.im == 1.3
+
+
+def test_get_ms2_spectra_mgf():
+    spectra = get_ms2_spectra("tests/data/test.mgf")
+    assert len(spectra) == 1
+    spectrum = spectra[0]
+    assert spectrum.identifier == "peptide1"
+    assert spectrum.mz[0] == pytest.approx(72.04439, 0.0001)
+    assert spectrum.intensity[0] == pytest.approx(100.0, 0.0001)
+    assert spectrum.mz[-1] == pytest.approx(423.11802, 0.0001)
+    assert spectrum.intensity[-1] == pytest.approx(200.0, 0.0001)
+
+
+def test_get_ms2_spectra_mzml():
+    spectra = get_ms2_spectra("tests/data/test.mzML")
+    assert len(spectra) == 4
+    spectrum = spectra[0]
+    assert spectrum.identifier == "index=2"
+    assert spectrum.mz[0] == pytest.approx(113.69136810302734, 0.0001)
+    assert spectrum.intensity[0] == pytest.approx(14.0, 0.0001)
+    assert spectrum.mz[-1] == pytest.approx(1699.74951171875, 0.0001)
+    assert spectrum.intensity[-1] == pytest.approx(15.0, 0.0001)
+
+
+def test_get_ms2_spectra_bruker_tdf():
+    spectra = get_ms2_spectra("tests/data/dda_test.d")
+    assert len(spectra) == 3
+    spectrum = spectra[0]
+    assert spectrum.identifier == "0"
+    assert spectrum.mz[0] == pytest.approx(199.7633514404297, 0.0001)
+    assert spectrum.intensity[0] == pytest.approx(162.0, 0.0001)
+
+
+def test_get_ms2_spectra_bruker_minitdf():
+    spectra = get_ms2_spectra("tests/data/test.ms2")
+    assert len(spectra) == 3
+    spectrum = spectra[0]
+    assert spectrum.identifier == "1"
+    assert spectrum.mz[0] == pytest.approx(190.1070556640625, 0.0001)
+    assert spectrum.intensity[0] == pytest.approx(350.0, 0.0001)