Merge branch 'develop' into 'master'

Release 1.0.1

See merge request tron/addannot!224

docs/requirements.txt

@@ -1,10 +1,11 @@
-Sphinx==4.2.0
-m2r2==0.3.1
-nbsphinx==0.8.7
-pandoc==1.1.0
-ipython==8.0.1
-ipykernel==5.3.4
+Sphinx==5.3.0
+m2r2==0.3.3
+nbsphinx==0.8.9
+pandoc==2.2
+ipython==7.27.0
+ipykernel==6.4.1
 #sphinx_rtd_theme==0.5.0
 #insipid_sphinx_theme==0.2.1
-pydata-sphinx-theme==0.7.1
-Jinja2==3.0.3
+pydata-sphinx-theme==0.11.0
+Jinja2==3.1.2
+markupsafe==2.1.1

neofox/__init__.py

@@ -18,7 +18,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
 
 
-VERSION = "1.0.0"
+VERSION = "1.0.1"
 
 
 REFERENCE_FOLDER_ENV = "NEOFOX_REFERENCE_FOLDER"

neofox/command_line.py

@@ -406,23 +406,26 @@ def _write_results_epitopes(neoepitopes: List[PredictedEpitope], output_folder,
     mhci_neoepitopes = [n for n in neoepitopes if ModelValidator.is_mhci_epitope(n)]
     mhcii_neoepitopes = [n for n in neoepitopes if ModelValidator.is_mhcii_epitope(n)]
 
-    ModelConverter.annotated_neoepitopes2epitopes_table(mhci_neoepitopes, mhc=neofox.MHC_I).to_csv(
-        os.path.join(
-            output_folder,
-            "{}_mhcI_epitope_candidates_annotated.tsv".format(output_prefix),
-        ),
-        sep="\t",
-        index=False,
-    )
-    ModelConverter.annotated_neoepitopes2epitopes_table(mhcii_neoepitopes, mhc=neofox.MHC_II).to_csv(
-        os.path.join(
-            output_folder,
-            "{}_mhcII_epitope_candidates_annotated.tsv".format(output_prefix),
-        ),
-        sep="\t",
-        index=False,
-    )
+    if mhci_neoepitopes:
+        ModelConverter.annotated_neoepitopes2epitopes_table(mhci_neoepitopes, mhc=neofox.MHC_I).to_csv(
+            os.path.join(
+                output_folder,
+                "{}_mhcI_epitope_candidates_annotated.tsv".format(output_prefix),
+            ),
+            sep="\t",
+            index=False,
+        )
+    if mhcii_neoepitopes:
+        ModelConverter.annotated_neoepitopes2epitopes_table(mhcii_neoepitopes, mhc=neofox.MHC_II).to_csv(
+            os.path.join(
+                output_folder,
+                "{}_mhcII_epitope_candidates_annotated.tsv".format(output_prefix),
+            ),
+            sep="\t",
+            index=False,
+        )
 
-    output_features = os.path.join(output_folder, "{}_neoepitope_candidates_annotated.json".format(output_prefix))
-    with open(output_features, "wb") as f:
-        f.write(json.dumps(ModelConverter.objects2json(neoepitopes)))
+    if neoepitopes:
+        output_features = os.path.join(output_folder, "{}_neoepitope_candidates_annotated.json".format(output_prefix))
+        with open(output_features, "wb") as f:
+            f.write(json.dumps(ModelConverter.objects2json(neoepitopes)))

neofox/tests/integration_tests/test_neofox_epitope.py

@@ -17,7 +17,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
 import os
-import unittest
 import pkg_resources
 import neofox.tests
 from neofox.command_line import _write_results_epitopes
@@ -145,6 +144,66 @@ def test_neofox_epitope_writing_output_table(self):
         self.assertTrue(os.path.exists(pkg_resources.resource_filename(
             neofox.tests.__name__, "resources/test_neoepitopes_mhcII_epitope_candidates_annotated.tsv")))
 
+    def test_neofox_epitope_writing_output_table_only_mhci(self):
+
+        neoepitopes = [
+            PredictedEpitope(
+                mutated_peptide="DEVLGEPSQDILVTDQTR",
+                wild_type_peptide="DEVLGEPSQDILVIDQTR",
+                isoform_mhc_i_i=self._get_test_mhcii_isoform("HLA-DRB1*01:01")
+            ),
+            PredictedEpitope(
+                mutated_peptide="DEVLGEPSQTILVTDQTR",
+                wild_type_peptide="DEVLGEPSQDILVIDQTR",
+                isoform_mhc_i_i=self._get_test_mhcii_isoform("HLA-DRB1*01:01")
+            ),
+        ]
+
+        annotated_neoepitopes = NeoFoxEpitope(
+            neoepitopes=neoepitopes,
+            num_cpus=4,
+        ).get_annotations()
+
+        _write_results_epitopes(
+            annotated_neoepitopes,
+            output_folder=pkg_resources.resource_filename(neofox.tests.__name__, "resources"),
+            output_prefix="test_neoepitopes_only_mhcii")
+
+        self.assertFalse(os.path.exists(pkg_resources.resource_filename(
+            neofox.tests.__name__, "resources/test_neoepitopes_only_mhcii_mhcI_epitope_candidates_annotated.tsv")))
+        self.assertTrue(os.path.exists(pkg_resources.resource_filename(
+            neofox.tests.__name__, "resources/test_neoepitopes_only_mhcii_mhcII_epitope_candidates_annotated.tsv")))
+
+    def test_neofox_epitope_writing_output_table_only_mhcii(self):
+
+        neoepitopes = [
+            PredictedEpitope(
+                mutated_peptide="DILVTDQTR",
+                wild_type_peptide="DILVIDQTR",
+                allele_mhc_i=self._get_test_mhci_allele('HLA-A*01:01'),
+            ),
+            PredictedEpitope(
+                mutated_peptide="DILVPDQTR",
+                wild_type_peptide="DILVIDQTR",
+                allele_mhc_i=self._get_test_mhci_allele('HLA-A*01:01'),
+            ),
+        ]
+
+        annotated_neoepitopes = NeoFoxEpitope(
+            neoepitopes=neoepitopes,
+            num_cpus=4,
+        ).get_annotations()
+
+        _write_results_epitopes(
+            annotated_neoepitopes,
+            output_folder=pkg_resources.resource_filename(neofox.tests.__name__, "resources"),
+            output_prefix="test_neoepitopes_only_mhci")
+
+        self.assertTrue(os.path.exists(pkg_resources.resource_filename(
+            neofox.tests.__name__, "resources/test_neoepitopes_only_mhci_mhcI_epitope_candidates_annotated.tsv")))
+        self.assertFalse(os.path.exists(pkg_resources.resource_filename(
+            neofox.tests.__name__, "resources/test_neoepitopes_only_mhci_mhcII_epitope_candidates_annotated.tsv")))
+
     def test_neofox_epitope_writing_output_table_with_patients(self):
 
         neoepitopes = [