Added unit tests. Preparation for v0.2.2.

Signed-off-by: JasonMendoza2008 <[email protected]>
MICS-Lab · Oct 28, 2022 · fca6851 · fca6851
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below.
           Lhotte, R., Usureau, C. & Taupin, J. (2022). Python Epitope Charge Calculator (PECC) package
-          (Version 0.2.1) [Computer software]. https://doi.org/10.5281/zenodo.7254809"
+          (Version 0.2.2) [Computer software]. https://doi.org/10.5281/zenodo.7254809"
 authors:
   - family-names: Lhotte
     given-names: Romain
@@ -13,7 +13,7 @@ authors:
     given-names: Jean-Luc
     orcid: https://orcid.org/0000-0002-5766-046X
 title: Python Epitope Charge Calculator
-version: 0.2.1
+version: 0.2.2
 doi: doi.org/10.5281/zenodo.7254809
 link: https://github.com/MICS-Lab/pecc
 date-released: 2022-10-26
diff --git a/README.md b/README.md
@@ -64,7 +64,7 @@ pecc\epitope_comparison_aux.py .
 pecc\output_type.py .                                                               [ 42%] 
 tests\__init__.py .                                                                 [ 47%] 
 tests\base_loading_for_tests.py .                                                   [ 52%] 
-tests\test_epitope_mismatches.py .....                                              [ 78%]
+tests\test_epitope_mismatches.py ......                                             [ 78%]
 tests\test_pecc.py ..                                                               [ 89%] 
 tests\test_unexpected_alleles.py ..                                                 [100%]
 ```
@@ -82,7 +82,7 @@ pecc\epitope_comparison_aux.py .
 pecc\output_type.py .                                                               [ 42%]
 tests\__init__.py .                                                                 [ 47%]
 tests\base_loading_for_tests.py .                                                   [ 52%]
-tests\test_epitope_mismatches.py .....                                              [ 78%]
+tests\test_epitope_mismatches.py ......                                             [ 78%]
 tests\test_pecc.py ..                                                               [ 89%]
 tests\test_unexpected_alleles.py ..                                                 [100%]
 ```
@@ -107,7 +107,7 @@ If you use this software, please cite it as below.
 
 - APA:
 ```
-Lhotte, R., Usureau, C., & Taupin, J. (2022). Python Epitope Charge Calculator (Version 0.2.1) [Computer software].
+Lhotte, R., Usureau, C., & Taupin, J. (2022). Python Epitope Charge Calculator (Version 0.2.2) [Computer software].
 https://doi.org/doi.org/10.5281/zenodo.7254809
 ```
 
@@ -118,7 +118,7 @@ author = {Lhotte, Romain and Usureau, Cédric and Taupin, Jean-Luc},
 doi = {doi.org/10.5281/zenodo.7254809},
 month = {10},
 title = {{Python Epitope Charge Calculator}},
-version = {0.2.1},
+version = {0.2.2},
 year = {2022}
 }
 ```
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pecc"
-version = "0.2.1"
+version = "0.2.2"
 description = "Python Epitopic Charge Calculator"
 authors = ["JasonMendoza2008 <[email protected]>"]
 readme = "README.md"

diff --git a/tests/test_epitope_mismatches.py b/tests/test_epitope_mismatches.py
@@ -60,8 +60,7 @@ def test_epitope_comparison_details() -> None:
     assert ("rq26Y" in list_mismatches_1)
     # rq26Y is in DQB1*03:01 but not in DQB1*03:02 (can be checked by aligning the sequences on
     # https://www.ebi.ac.uk/ipd/imgt/hla/alignment/)
-    # The prediction does not output rq26Y although it should
-    # rq26Y is therefore a false negative
+    # The prediction does not output rq26Y although it should - rq26Y is therefore a false negative
     assert ("rqp37YA" not in list_mismatches_1)
     # Both have this eplet
     assert ("rp37FV" not in list_mismatches_1)
@@ -198,3 +197,33 @@ def test_epitope_comparison_dr13() -> None:
     assert ("85VV_DR" in output_df_fn.at[8, "EpMismatches"])
 
     os.remove(f"{output_path}.csv")
+
+
+def test_interlocus2() -> None:
+    donordf, recipientdf, output_path = base_loading("pytest.xlsx", "False Negs")
+
+    compute_epitopic_charge(
+        donordf,
+        recipientdf,
+        output_path,
+        OutputType.ONLY_DETAILS,
+        True,
+        True,
+        False,
+        exclude=None,
+        interlocus2=False
+    )
+
+    output_df_fn: pd.DataFrame = pd.read_csv(f"{output_path}.csv", index_col="Index")
+
+    for index_ in range(6, 2146):
+        assert output_df_fn.at[index_, "EpMismatches"] == "None"
+
+    list_mismatches_1: list[str] = output_df_fn.at[1, "EpMismatches"].split(", ")
+    assert ("rq26Y" not in list_mismatches_1)
+    # rq26Y is in DQB1*03:01 but not in DQB1*03:02 (can be checked by aligning the sequences on
+    # https://www.ebi.ac.uk/ipd/imgt/hla/alignment/)
+    # The prediction does not output rq26Y although it should - rq26Y is therefore a false negative
+    # But we don't want interlocus2 (argument interlocus2 = False).
+
+    os.remove(f"{output_path}.csv")
diff --git a/tests/test_pecc.py b/tests/test_pecc.py
@@ -2,4 +2,4 @@
 
 
 def test_version():
-    assert __version__ == '0.2.1'
+    assert __version__ == '0.2.2'
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,4 @@


		def test_version():
		assert __version__ == '0.2.1'
		assert __version__ == '0.2.2'