add test clustalw

jamesmkrieger · Dec 3, 2024 · a7e57c4 · a7e57c4
1 parent cb1778a
commit a7e57c4
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -31,6 +31,7 @@ jobs:
         source activate test
         conda install --yes numpy scipy nose requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer mdtraj; fi
+        conda install -c bioconda clustalw
         pip install mmtf-python scikit-learn
         pip install .
         python setup.py build_ext --inplace --force

diff --git a/prody/tests/sequence/test_analysis.py b/prody/tests/sequence/test_analysis.py
@@ -1202,11 +1202,19 @@ def testMATLAB10(self):
 class TestBuildMSA(TestCase):
 
     def testBuildMSAlocal(self):
-        sequences = [ags[0].protein["A"].getSequence(), 
+        sequences = [ags[0].protein["A"].getSequence(),
                      ags[1].protein["A"].getSequence()]
 
         expect1 = parseMSA(pathDatafile('msa_3hsyA_3o21A.fasta'))
         expect2 = parseMSA(pathDatafile('msa_3hsyA_3o21A_new.fasta'))
         result = buildMSA(sequences, method="local", labels=["A2", "A3"])
         assert result in (expect1, expect2), "The list of expected buildMSA results did not contain " + result
-
+
+    def testBuildMSAclustalw(self):
+        sequences = [ags[0].protein["A"].getSequence(),
+                     ags[1].protein["A"].getSequence()]
+
+        expect1 = parseMSA(pathDatafile('msa_3hsyA_3o21A.fasta'))
+        expect2 = parseMSA(pathDatafile('msa_3hsyA_3o21A_new.fasta'))
+        result = buildMSA(sequences, method="clustalw", labels=["A2", "A3"])
+        assert result in (expect1, expect2), "The list of expected buildMSA results did not contain " + result