[FIX] Decoding ontology in PeptideIdentification df conversion (#5659)

* fix tuple creation

* add pep evidence export

* update test

* add pep evidence concatenation test

* change dtype for pep evidences to U1000

* fix error while decoding ontology

* simple test without decode_ontology

src/pyOpenMS/pyopenms/dataframes.py

@@ -288,11 +288,14 @@ def get_key(val):
                 return key
     dmv = [default_missing_values[get_key(t)] for t in types]
 
-    decodedMVs = [m.decode("utf-8") for m in metavals] if decode_ontology else metavals
-    cv = ControlledVocabulary()
-    cv.loadFromOBO("psims", File.getOpenMSDataPath() + "/CV/psi-ms.obo")
-    clearMVs = [cv.getTerm(m).name if m.startswith("MS:") else m for m in decodedMVs]
-    #cols = ["id", "RT", "mz", "score", "charge"] + decodedMVs
+    decodedMVs = [m.decode("utf-8") for m in metavals]
+    if decode_ontology:
+        cv = ControlledVocabulary()
+        cv.loadFromOBO("psims", File.getOpenMSDataPath() + "/CV/psi-ms.obo")
+        clearMVs = [cv.getTerm(m).name if m.startswith("MS:") else m for m in decodedMVs]
+    else:
+        clearMVs = decodedMVs
+
     clearcols = ["id", "RT", "mz", mainscorename, "charge", "protein_accession", "start", "end"] + clearMVs
     coltypes = ['U100', 'f', 'f', 'f', 'i','U1000', 'U1000', 'U1000'] + types
     dt = list(zip(clearcols, coltypes))

src/pyOpenMS/tests/unittests/test000.py

@@ -2278,6 +2278,7 @@ def test_peptide_identifications_to_df():
     peps.append(p1)
 
     assert pyopenms.peptide_identifications_to_df(peps).shape == (2,10)
+    assert pyopenms.peptide_identifications_to_df(peps, decode_ontology=False).shape == (2,10)
     assert pyopenms.peptide_identifications_to_df(peps)['protein_accession'][0] == 'sp|Accession1,sp|Accession2'
     assert pyopenms.peptide_identifications_to_df(peps, export_unidentified=False).shape == (1,10)