Mercurial > repos > chrisb > gap_all_glycan_tools
view manipulate/minimal_kcf/test_minimal_kcf.py @ 1:0a5e0df17054 draft default tip
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| author | chrisb |
|---|---|
| date | Fri, 06 May 2016 08:05:48 -0400 |
| parents | 89592faa2875 |
| children |
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__license__ = "MIT" import unittest import minimal_kcf as mk class SimpleUnitTest(unittest.TestCase): def setUp(self): import os self.kcinput = {"ringsmcaw": """ENTRY G04845 Glycan COMPOSITION (Gal)3 (Glc)1 (GlcNAc)2 (LFuc)2 (Neu5Ac)1 MASS 1656.5 DBLINKS CCSD: 23949 GlycomeDB: 20420 JCGGDB: JCGG-STR011245 NODE 9 1 Glc 0 0 2 Gal -10 0 3 GlcNAc -20 10 4 GlcNAc -20 -10 5 Gal -30 15 6 LFuc -30 5 7 LFuc -30 -5 8 Gal -30 -15 9 Neu5Ac -40 15 EDGE 8 1 2:b1 1:4 2 3:b1 2:6 3 4:b1 2:3 4 5:b1 3:4 5 6:a1 3:3 6 7:a1 4:4 7 8:b1 4:3 8 9:a2 5:3 /// ENTRY G05108 Glycan COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)1 (S)1 MASS 1266.2 CLASS Glycoprotein; O-Glycan DBLINKS CCSD: 33353 GlycomeDB: 20590 JCGGDB: JCGG-STR011425 NODE 7 1 GalNAc 20 1 2 Gal 10 1 3 GlcNAc 0 1 4 S -5 5 5 Gal -10 1 6 LFuc -10 -4 7 Neu5Ac -20 1 EDGE 6 1 2:b1 1:3 2 3:b1 2:3 3 4 3:6 4 5:b1 3:4 5 6:a1 3:3 6 7:a2 5:3 /// ENTRY G05121 Glycan COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)2 MASS 1477.3 CLASS Glycoprotein; O-Glycan DBLINKS CCSD: 33350 GlycomeDB: 20599 JCGGDB: JCGG-STR011433 NODE 7 1 GalNAc 0 0 2 Neu5Ac -10 5 3 Gal -10 -5 4 GlcNAc -20 -5 5 Gal -30 0 6 LFuc -30 -10 7 Neu5Ac -40 0 EDGE 6 1 2:a2 1:6 2 3:b1 1:3 3 4:b1 3:3 4 5:b1 4:4 5 6:a1 4:3 6 7:a2 5:3 /// ENTRY G04183 Glycan COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3 MASS 3026.8 CLASS Glycoprotein; N-Glycan DBLINKS CCSD: 41981 GlycomeDB: 19974 JCGGDB: JCGG-STR010756 NODE 15 1 GlcNAc 0 0 2 GlcNAc -10 0 3 Man -20 0 4 Man -30 10 5 Man -30 -10 6 GlcNAc -40 10 7 GlcNAc -40 -5 8 GlcNAc -40 -15 9 Gal -50 10 10 Gal -50 0 11 LFuc -50 -10 12 Gal -50 -15 13 Neu5Ac -60 10 14 Neu5Ac -60 0 15 Neu5Ac -60 -15 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:6 13 14:a2 10:3 14 15:a2 12:6 /// ENTRY G04329 Glycan COMPOSITION (Gal)3 (GlcNAc)3 (LFuc)3 (Neu5Ac)1 MASS 1843.7 DBLINKS CCSD: 36620 GlycomeDB: 20084 JCGGDB: JCGG-STR010874 NODE 10 1 GlcNAc 27 -5 2 Gal 18 0 3 LFuc 18 -10 4 GlcNAc 9 0 5 Gal 0 5 6 LFuc 0 -5 7 GlcNAc -9 5 8 Gal -18 10 9 LFuc -18 0 10 Neu5Ac -27 10 EDGE 9 1 2:b1 1:4 2 3:a1 1:3 3 4:b1 2:3 4 5:b1 4:4 5 6:a1 4:3 6 7:b1 5:3 7 8:b1 7:4 8 9:a1 7:3 9 10:a2 8:3 /// ENTRY G04804 Glycan COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3 MASS 3026.8 CLASS Glycoprotein; N-Glycan REFERENCE 1 [PMID:6704968] Chandrasekaran EV, Davila M, Nixon D, Mendicino J. Structures of the oligosaccharide chains of two forms of alpha 1-acid glycoprotein purified from liver metastases of lung, colon, and breast tumors. Cancer. Res. 44 (1984) 1557-67. DBLINKS CCSD: 8168 GlycomeDB: 33225 JCGGDB: JCGG-STR024138 NODE 15 1 GlcNAc 27.2 1.6 2 GlcNAc 17.2 1.6 3 Man 8.2 1.6 4 Man 0.2 7.6 5 Man 0.2 -4.4 6 GlcNAc -8.8 7.6 7 GlcNAc -8.8 -0.4 8 GlcNAc -8.8 -8.4 9 Gal -17.8 7.6 10 Gal -17.8 3.6 11 LFuc -17.8 -4.4 12 Gal -17.8 -8.4 13 Neu5Ac -26.8 7.6 14 Neu5Ac -26.8 3.6 15 Neu5Ac -26.8 -8.4 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:3 13 14:a2 10:3 14 15:a2 12:6 /// """, "ringsmcaw_modified": """ENTRY G04845 Glycan NODE 9 1 Glc 0 0 2 Gal -10 0 3 GlcNAc -20 10 4 GlcNAc -20 -10 5 Gal -30 15 6 LFuc -30 5 7 LFuc -30 -5 8 Gal -30 -15 9 Neu5Ac -40 15 EDGE 8 1 2:b1 1:4 2 3:b1 2:6 3 4:b1 2:3 4 5:b1 3:4 5 6:a1 3:3 6 7:a1 4:4 7 8:b1 4:3 8 9:a2 5:3 /// ENTRY G05108 Glycan NODE 7 1 GalNAc 20 1 2 Gal 10 1 3 GlcNAc 0 1 4 S -5 5 5 Gal -10 1 6 LFuc -10 -4 7 Neu5Ac -20 1 EDGE 6 1 2:b1 1:3 2 3:b1 2:3 3 4 3:6 4 5:b1 3:4 5 6:a1 3:3 6 7:a2 5:3 /// ENTRY G05121 Glycan NODE 7 1 GalNAc 0 0 2 Neu5Ac -10 5 3 Gal -10 -5 4 GlcNAc -20 -5 5 Gal -30 0 6 LFuc -30 -10 7 Neu5Ac -40 0 EDGE 6 1 2:a2 1:6 2 3:b1 1:3 3 4:b1 3:3 4 5:b1 4:4 5 6:a1 4:3 6 7:a2 5:3 /// ENTRY G04183 Glycan NODE 15 1 GlcNAc 0 0 2 GlcNAc -10 0 3 Man -20 0 4 Man -30 10 5 Man -30 -10 6 GlcNAc -40 10 7 GlcNAc -40 -5 8 GlcNAc -40 -15 9 Gal -50 10 10 Gal -50 0 11 LFuc -50 -10 12 Gal -50 -15 13 Neu5Ac -60 10 14 Neu5Ac -60 0 15 Neu5Ac -60 -15 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:6 13 14:a2 10:3 14 15:a2 12:6 /// ENTRY G04329 Glycan NODE 10 1 GlcNAc 27 -5 2 Gal 18 0 3 LFuc 18 -10 4 GlcNAc 9 0 5 Gal 0 5 6 LFuc 0 -5 7 GlcNAc -9 5 8 Gal -18 10 9 LFuc -18 0 10 Neu5Ac -27 10 EDGE 9 1 2:b1 1:4 2 3:a1 1:3 3 4:b1 2:3 4 5:b1 4:4 5 6:a1 4:3 6 7:b1 5:3 7 8:b1 7:4 8 9:a1 7:3 9 10:a2 8:3 /// ENTRY G04804 Glycan NODE 15 1 GlcNAc 27.2 1.6 2 GlcNAc 17.2 1.6 3 Man 8.2 1.6 4 Man 0.2 7.6 5 Man 0.2 -4.4 6 GlcNAc -8.8 7.6 7 GlcNAc -8.8 -0.4 8 GlcNAc -8.8 -8.4 9 Gal -17.8 7.6 10 Gal -17.8 3.6 11 LFuc -17.8 -4.4 12 Gal -17.8 -8.4 13 Neu5Ac -26.8 7.6 14 Neu5Ac -26.8 3.6 15 Neu5Ac -26.8 -8.4 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:3 13 14:a2 10:3 14 15:a2 12:6 /// """, "ringsfinger": """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 /// """, "ringsbroken": """ABCDEFGENTRY G00015 Glycan NODE 8 1 Asn 20 0 2 GlcNAc 12 0 """ } self.kcoutput={"ringsmcaw":"""ENTRY G04845 Glycan NODE 9 1 Glc 0 0 2 Gal -10 0 3 GlcNAc -20 10 4 GlcNAc -20 -10 5 Gal -30 15 6 LFuc -30 5 7 LFuc -30 -5 8 Gal -30 -15 9 Neu5Ac -40 15 EDGE 8 1 2:b1 1:4 2 3:b1 2:6 3 4:b1 2:3 4 5:b1 3:4 5 6:a1 3:3 6 7:a1 4:4 7 8:b1 4:3 8 9:a2 5:3 /// ENTRY G05108 Glycan NODE 7 1 GalNAc 20 1 2 Gal 10 1 3 GlcNAc 0 1 4 S -5 5 5 Gal -10 1 6 LFuc -10 -4 7 Neu5Ac -20 1 EDGE 6 1 2:b1 1:3 2 3:b1 2:3 3 4 3:6 4 5:b1 3:4 5 6:a1 3:3 6 7:a2 5:3 /// ENTRY G05121 Glycan NODE 7 1 GalNAc 0 0 2 Neu5Ac -10 5 3 Gal -10 -5 4 GlcNAc -20 -5 5 Gal -30 0 6 LFuc -30 -10 7 Neu5Ac -40 0 EDGE 6 1 2:a2 1:6 2 3:b1 1:3 3 4:b1 3:3 4 5:b1 4:4 5 6:a1 4:3 6 7:a2 5:3 /// ENTRY G04183 Glycan NODE 15 1 GlcNAc 0 0 2 GlcNAc -10 0 3 Man -20 0 4 Man -30 10 5 Man -30 -10 6 GlcNAc -40 10 7 GlcNAc -40 -5 8 GlcNAc -40 -15 9 Gal -50 10 10 Gal -50 0 11 LFuc -50 -10 12 Gal -50 -15 13 Neu5Ac -60 10 14 Neu5Ac -60 0 15 Neu5Ac -60 -15 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:6 13 14:a2 10:3 14 15:a2 12:6 /// ENTRY G04329 Glycan NODE 10 1 GlcNAc 27 -5 2 Gal 18 0 3 LFuc 18 -10 4 GlcNAc 9 0 5 Gal 0 5 6 LFuc 0 -5 7 GlcNAc -9 5 8 Gal -18 10 9 LFuc -18 0 10 Neu5Ac -27 10 EDGE 9 1 2:b1 1:4 2 3:a1 1:3 3 4:b1 2:3 4 5:b1 4:4 5 6:a1 4:3 6 7:b1 5:3 7 8:b1 7:4 8 9:a1 7:3 9 10:a2 8:3 /// ENTRY G04804 Glycan NODE 15 1 GlcNAc 27.2 1.6 2 GlcNAc 17.2 1.6 3 Man 8.2 1.6 4 Man 0.2 7.6 5 Man 0.2 -4.4 6 GlcNAc -8.8 7.6 7 GlcNAc -8.8 -0.4 8 GlcNAc -8.8 -8.4 9 Gal -17.8 7.6 10 Gal -17.8 3.6 11 LFuc -17.8 -4.4 12 Gal -17.8 -8.4 13 Neu5Ac -26.8 7.6 14 Neu5Ac -26.8 3.6 15 Neu5Ac -26.8 -8.4 EDGE 14 1 2:b1 1:4 2 3:b1 2:4 3 4:a1 3:6 4 5:a1 3:3 5 6:b1 4:2 6 7:b1 5:4 7 8:b1 5:2 8 9:b1 6:4 9 10:b1 7:4 10 11:a1 7:3 11 12:b1 8:4 12 13:a2 9:3 13 14:a2 10:3 14 15:a2 12:6 /// """} os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http: pass def tearDown(self): pass def test_simple_kcf(self): import StringIO kcinput = """ENTRY X Glycan NODE 2 1 galnac 0 0 2 gal -8 0 EDGE 1 1 2:1 1 /// """ kchandle = StringIO.StringIO(''.join(kcinput)) h = mk.read_meta_kcf(kchandle) i = mk.flatten_meta_kcf_list(h) self.assertIn("ENTRY X Glycan\n", i) self.assertIn("NODE 2\n", i) self.assertIn(" 1 2:1 1\n", i) def test_multiple_kcf(self): import StringIO kcinput = """ENTRY ((A??)AN) Glycan NODE 2 1 galnac 0 0 2 gal -8 0 EDGE 1 1 2:1 1 /// ENTRY G00005 Glycan NODE 6 1 PP-Dol 15 1 2 GlcNAc 8 1 3 GlcNAc 0 1 4 Man -9 1 5 Man -16 7 6 Man -16 -6 EDGE 5 1 2:a1 1 2 3:b1 2:4 3 4:b1 3:4 4 5:a1 4:6 5 6:a1 4:3 /// """ kchandle = StringIO.StringIO(''.join(kcinput)) h = mk.read_meta_kcf(kchandle) i = mk.flatten_meta_kcf_list(h) self.assertIn(" 1 2:1 1\n", i) self.assertIn(" 5 6:a1 4:3\n", i) def test_empty_stream(self): with self.assertRaises(IOError): m = mk.read_meta_kcf(None) with self.assertRaises(IOError): m = mk.read_meta_kcf([]) with self.assertRaises(IOError): m = mk.read_meta_kcf("") def test_mcaw_kcf(self): import StringIO kcf = self.kcinput["ringsmcaw"] handle = StringIO.StringIO(''.join(kcf)) h = mk.read_meta_kcf(handle) i = mk.flatten_meta_kcf_list(h) self.assertEqual(i,self.kcoutput["ringsmcaw"]) def run_tests(): unittest.main() if __name__ == '__main__': run_tests()