return most recent genome build for the pipeline config file.

[htsworkflow.git] / gaworkflow / pipeline / test / test_genome_mapper.py

diff --git a/gaworkflow/pipeline/test/test_genome_mapper.py b/gaworkflow/pipeline/test/test_genome_mapper.py
new file mode 100644 (file)
index 0000000..c8366d1
--- /dev/null
+++ b/gaworkflow/pipeline/test/test_genome_mapper.py
@@ -0,0 +1,33 @@
+import unittest
+
+from StringIO import StringIO
+from gaworkflow.pipeline import genome_mapper
+
+class testGenomeMapper(unittest.TestCase):
+    def test_construct_mapper(self):
+        genomes = {
+        'Arabidopsis thaliana': {'v01212004': '/arabidopsis'},
+        'Homo sapiens': {'hg18': '/hg18'},
+        'Mus musculus': {'mm8': '/mm8',
+                        'mm9': '/mm9',
+                        'mm10': '/mm10'},
+        'Phage': {'174': '/phi'},
+        }
+        genome_map = genome_mapper.constructMapperDict(genomes)
+        
+        self.failUnlessEqual("%(Mus musculus|mm8)s" % (genome_map), "/mm8")
+        self.failUnlessEqual("%(Phage|174)s" % (genome_map), "/phi")
+        self.failUnlessEqual("%(Mus musculus)s" % (genome_map), "/mm10")
+        self.failUnlessEqual("%(Mus musculus|mm8)s" % (genome_map), "/mm8")
+        self.failUnlessEqual("%(Mus musculus|mm10)s" % (genome_map), "/mm10")
+        
+        self.failUnlessEqual(len(genome_map.keys()), 6)
+        self.failUnlessEqual(len(genome_map.values()), 6)
+        self.failUnlessEqual(len(genome_map.items()), 6)
+        
+        
+def suite():
+    return unittest.makeSuite(testGenomeMapper,'test')
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")