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test_SCOP_Scop.py

# Copyright 2001 by Gavin E. Crooks.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Unit test for Scop"""

import unittest
from StringIO import *

from Bio.SCOP import *



00015 class ScopTests(unittest.TestCase):


    def testParse(self):
  
        f = open("./SCOP/dir.cla.scop.txt_test")
        try:
            cla = f.read()
            f.close()
            
            f = open("./SCOP/dir.des.scop.txt_test")
            des = f.read()
            f.close()

            f = open("./SCOP/dir.hie.scop.txt_test")
            hie = f.read()
        finally:
            f.close()

        scop = Scop(StringIO(cla), StringIO(des), StringIO(hie))

        cla_out = StringIO()
        scop.write_cla(cla_out)
        self.assertEqual(cla_out.getvalue(), cla)
        
        des_out = StringIO()
        scop.write_des(des_out)
        self.assertEqual(des_out.getvalue(), des)

        hie_out = StringIO()
        scop.write_hie(hie_out)
        self.assertEqual(hie_out.getvalue(), hie)

        domain = scop.getDomainBySid("d1hbia_")
        self.assertEqual(domain.sunid, 14996)

        domains = scop.getDomains()
        self.assertEqual(len(domains), 14)
        self.assertEqual(domains[4].sunid, 14988)


        dom = scop.getNodeBySunid(-111)
        self.assertEqual(dom, None)
        dom = scop.getDomainBySid("no such domain")
        self.assertEqual(dom, None)
                


    def testSccsOrder(self):
        self.assertEqual(cmp_sccs("a.1.1.1", "a.1.1.1"), 0)
        self.assertEqual(cmp_sccs("a.1.1.2", "a.1.1.1"), 1)
        self.assertEqual(cmp_sccs("a.1.1.2", "a.1.1.11"), -1)
        self.assertEqual(cmp_sccs("a.1.2.2", "a.1.1.11"), 1)
        self.assertEqual(cmp_sccs("a.1.2.2", "a.5.1.11"), -1)
        self.assertEqual(cmp_sccs("b.1.2.2", "a.5.1.11"), 1)
        self.assertEqual(cmp_sccs("b.1.2.2", "b.1.2"), 1)

    def testParseDomain(self):
        s=">d1tpt_1 a.46.2.1 (1-70) Thymidine phosphorylase {Escherichia coli}"
        dom = parse_domain(s)

        self.assertEqual(dom.sid, 'd1tpt_1')
        self.assertEqual(dom.sccs, 'a.46.2.1')
        self.assertEqual(dom.residues.pdbid, '1tpt')
        self.assertEqual(dom.description, 'Thymidine phosphorylase {Escherichia coli}')

        s2="d1tpt_1 a.46.2.1 (1tpt 1-70) Thymidine phosphorylase {E. coli}"
        self.assertEqual(s2, str(parse_domain(s2)))



        #Genetic domains (See Astral release notes)
        s3="g1cph.1 g.1.1.1 (1cph B:,A:) Insulin {Cow (Bos taurus)}"
        self.assertEqual(s3, str(parse_domain(s3)))

        s4="e1cph.1a g.1.1.1 (1cph A:) Insulin {Cow (Bos taurus)}"
        self.assertEqual(s4, str(parse_domain(s4)))

        #Raw Astral header
        s5=">e1cph.1a g.1.1.1 (A:) Insulin {Cow (Bos taurus)}"
        self.assertEqual(s4,  str(parse_domain(s5)))

        self.assertRaises(ValueError, parse_domain, "Totally wrong")

    def testConstructFromDirectory(self):
        scop = Scop (dir_path="SCOP", version="test")
        self.assertTrue(isinstance(scop, Scop))
         
        domain = scop.getDomainBySid("d1hbia_")
        self.assertEqual(domain.sunid, 14996)
         
    def testGetAscendent(self):
        scop = Scop (dir_path="SCOP", version="test")
        domain = scop.getDomainBySid("d1hbia_")

        # get the fold
        fold = domain.getAscendent('cf')
        self.assertEqual(fold.sunid, 46457)
        
        #get the superfamily
        sf = domain.getAscendent('superfamily')
        self.assertEqual(sf.sunid, 46458)

        # px has no px ascendent
        px = domain.getAscendent('px')
        self.assertEqual(px, None)

        # an sf has no px ascendent
        px2 = sf.getAscendent('px')
        self.assertEqual(px2, None)


00127     def test_get_descendents(self):
        """Test getDescendents method"""
        scop = Scop (dir_path="SCOP", version="test")
        fold = scop.getNodeBySunid(46457)

        # get px descendents
        domains = fold.getDescendents('px')
        self.assertEqual(len(domains), 14)
        for d in domains:
            self.assertEqual(d.type, 'px')
            
        sfs = fold.getDescendents('superfamily')
        self.assertEqual(len(sfs), 1)
        for d in sfs:
            self.assertEqual(d.type, 'sf')

        # cl has no cl descendent
        cl = fold.getDescendents('cl')
        self.assertEqual(cl, [])
        
        


if __name__=='__main__':
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)

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