Add tests for backtranslator module

tests/test_backtranslator.py

@@ -0,0 +1,116 @@
+"""
+Tests for the mutalyzer.backtranslator module.
+"""
+
+
+from __future__ import unicode_literals
+
+import pytest
+
+from mutalyzer.backtranslator import backtranslate
+import mutalyzer.Retriever
+
+from fixtures import with_links, with_references
+
+
+DIVERSIONS = {
+    'NM_003002': 'NM_003002.2'
+}
+
+
+@pytest.fixture
+def divert(monkeypatch, request):
+    """
+    Ad-hoc fixture diverting a retriever call for NM_003002 to NM_003002.2.
+
+    This is useful to mimic behaviour of the retriever for the accession
+    without version number, which we cannot do with a normal fixture (the
+    retriever does not support non-versioned references in the database).
+    """
+    loadrecord = mutalyzer.Retriever.GenBankRetriever.loadrecord
+    def mock_loadrecord(self, identifier):
+        identifier = DIVERSIONS.get(identifier, identifier)
+        return loadrecord(self, identifier)
+    monkeypatch.setattr(mutalyzer.Retriever.GenBankRetriever, 'loadrecord', mock_loadrecord)
+
+
+@with_references('NM_003002.2')
+def test_nm(output):
+    """
+    Back translate on NM.
+    """
+    variants = backtranslate(output, 'NM_003002.2:p.Asp92Tyr')
+    assert sorted(variants) == ['NM_003002.2:c.274G>T']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
+
+
+@with_references('NM_003002.2')
+@pytest.mark.usefixtures('divert')
+def test_nm_no_version(output):
+    """
+    Back translate on NM.
+    """
+    variants = backtranslate(output, 'NM_003002:p.Asp92Tyr')
+    assert sorted(variants) == ['NM_003002:c.274G>T']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
+
+
+@with_links(('NM_003002.2', 'NP_002993.1'))
+@with_references('NM_003002.2')
+def test_np(output):
+    """
+    Back translate on NP.
+    """
+    variants = backtranslate(output, 'NP_002993.1:p.Asp92Glu')
+    assert sorted(variants) == ['NM_003002.2:c.276C>A',
+                                'NM_003002.2:c.276C>G']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
+
+
+@with_links(('NM_003002', 'NP_002993'))
+@with_references('NM_003002.2')
+@pytest.mark.usefixtures('divert')
+def test_np_no_version(output):
+    """
+    Back translate on NP.
+    """
+    variants = backtranslate(output, 'NP_002993:p.Asp92Glu')
+    assert sorted(variants) == ['NM_003002:c.276C>A',
+                                'NM_003002:c.276C>G']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 1
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
+
+
+@with_links((None, 'NP_000000.0'))
+def test_np_no_nm(output):
+    """
+    Back translate on NP without NM.
+    """
+    variants = backtranslate(output, 'NP_000000.0:p.Asp92Tyr')
+    assert sorted(variants) == ['UNKNOWN:c.274G>T']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 1
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
+
+
+@with_links((None, 'NP_000000.0'))
+def test_np_no_nm_improvable(output):
+    """
+    Back translate on NP without NM improvable.
+    """
+    variants = backtranslate(output, 'NP_000000.0:p.Leu92Phe')
+    assert sorted(variants) == ['UNKNOWN:c.274C>T',
+                                'UNKNOWN:c.276A>C',
+                                'UNKNOWN:c.276A>T',
+                                'UNKNOWN:c.276G>C',
+                                'UNKNOWN:c.276G>T']
+    assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
+    assert len(output.getMessagesWithErrorCode('WNODNA')) == 1
+    assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 1