Mercurial > repos > chrisb > gap_all_glycan_tools
view extract_display_features/rings_fingerprinter/test_fingerprinter.py @ 0:89592faa2875 draft
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| author | chrisb |
|---|---|
| date | Wed, 23 Mar 2016 14:35:56 -0400 |
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__license__ = "MIT" import unittest import post_fingerprinter as fp class SimpleUnitTest(unittest.TestCase): def setUp(self): import os self.kcinput = {"rings": """ENTRY G00015 Glycan NODE 8 1 Asn 20 0 2 GlcNAc 12 0 3 GlcNAc 3 0 4 Man -5 0 5 Man -12 5 6 Man -12 -5 7 GlcNAc -20 5 8 GlcNAc -20 -5 EDGE 7 1 2:b1 1 2 3:b1 2:4 3 4:b1 3:4 4 5:a1 4:6 5 6:a1 4:3 6 7:b1 5:2 7 8:b1 6:2 /// ENTRY G00016 Glycan NODE 9 1 Asn 20 3 2 GlcNAc 12 3 3 LFuc 4 8 4 GlcNAc 3 -2 5 Man -5 -2 6 Man -12 3 7 Man -12 -7 8 GlcNAc -20 3 9 GlcNAc -20 -7 EDGE 8 1 2:b1 1 2 3:a1 2:6 3 4:b1 2:4 4 5:b1 4:4 5 6:a1 5:6 6 7:a1 5:3 7 8:b1 6:2 8 9:b1 7:2 /// ENTRY G00017 Glycan NODE 11 1 Asn 24 3 2 GlcNAc 14 3 3 LFuc 7 8 4 GlcNAc 6 -2 5 Man -2 -2 6 Man -8 3 7 Man -8 -7 8 GlcNAc -16 3 9 GlcNAc -16 -7 10 Gal -24 3 11 Gal -24 -7 EDGE 10 1 2:b1 1 2 3:a1 2:6 3 4:b1 2:4 4 5:b1 4:4 5 6:a1 5:6 6 7:a1 5:3 7 8:b1 6:2 8 9:b1 7:2 9 10:b1 8:4 10 11:b1 9:4 /// ENTRY G00018 Glycan NODE 13 1 Asn 28 3 2 GlcNAc 18 3 3 LFuc 10 8 4 GlcNAc 9 -2 5 Man 1 -2 6 Man -5 4 7 Man -5 -8 8 GlcNAc -13 4 9 GlcNAc -13 -8 10 Gal -21 4 11 Gal -21 -8 12 Neu5Ac -29 4 13 Neu5Ac -29 -8 EDGE 12 1 2:b1 1 2 3:a1 2:6 3 4:b1 2:4 4 5:b1 4:4 5 6:a1 5:6 6 7:a1 5:3 7 8:b1 6:2 8 9:b1 7:2 9 10:b1 8:4 10 11:b1 9:4 11 12:a2 10:6 12 13:a2 11:6 /// ENTRY G00019 Glycan NODE 9 1 Asn 20 0 2 GlcNAc 12 0 3 GlcNAc 3 0 4 Man -5 0 5 Man -12 5 6 Man -12 -5 7 GlcNAc -15 0 8 GlcNAc -20 5 9 GlcNAc -20 -5 EDGE 8 1 2:b1 1 2 3:b1 2:4 3 4:b1 3:4 4 5:a1 4:6 5 6:a1 4:3 6 7:b1 4:4 7 8:b1 5:2 8 9:b1 6:2 /// ENTRY G00020 Glycan NODE 9 1 Asn 20 3 2 GlcNAc 11 3 3 GlcNAc 2 3 4 Man -6 3 5 Man -13 9 6 Man -13 -3 7 GlcNAc -21 9 8 GlcNAc -21 2 9 GlcNAc -21 -8 EDGE 8 1 2:b1 1 2 3:b1 2:4 3 4:b1 3:4 4 5:a1 4:6 5 6:a1 4:3 6 7:b1 5:2 7 8:b1 6:4 8 9:b1 6:2 /// """ } self.similaritymatrix = { "rings": """G00015\t 1.000000\t 0.777778\t 0.460526\t 0.304348\t 0.564516\t 0.636364\t \nG00016\t 0.777778\t 1.000000\t 0.592105\t 0.391304\t 0.486111\t 0.538462\t \nG00017\t 0.460526\t 0.592105\t 1.000000\t 0.660870\t 0.339806\t 0.378947\t \nG00018\t 0.304348\t 0.391304\t 0.660870\t 1.000000\t 0.255319\t 0.268657\t \nG00019\t 0.564516\t 0.486111\t 0.339806\t 0.255319\t 1.000000\t 0.444444\t \nG00020\t 0.636364\t 0.538462\t 0.378947\t 0.268657\t 0.444444\t 1.000000\t """ } os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http: pass def tearDown(self): pass def test_kcf_input(self): import StringIO kchandle = StringIO.StringIO(''.join(self.kcinput["rings"])) h = fp.post_rings_fingerprinter(kchandle) # print h d = fp.extract_dendro_from_fingerprinter_output(h) # print d self.assertIn(self.similaritymatrix["rings"], h) self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", h) self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", d) def test_empty_stream(self): with self.assertRaises(IOError): fp.post_rings_fingerprinter(None) with self.assertRaises(IOError): fp.post_rings_fingerprinter([]) with self.assertRaises(IOError): fp.post_rings_fingerprinter("") with self.assertRaises(IOError): fp.extract_dendro_from_fingerprinter_output(None) with self.assertRaises(IOError): fp.extract_dendro_from_fingerprinter_output([]) with self.assertRaises(IOError): fp.extract_dendro_from_fingerprinter_output("") def run_tests(): unittest.main() if __name__ == '__main__': run_tests()