From 7feaf88936f49aa3316912b8505836a0a200eb1b Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 8 Oct 2015 16:06:07 +0200
Subject: [PATCH] Add tests for backtranslator module
---
tests/test_backtranslator.py | 116 +++++++++++++++++++++++++++++++++++
1 file changed, 116 insertions(+)
create mode 100644 tests/test_backtranslator.py
diff --git a/tests/test_backtranslator.py b/tests/test_backtranslator.py
new file mode 100644
index 00000000..8799f018
--- /dev/null
+++ b/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
--
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