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# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. 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 io import StringIO
from Bio.SCOP import cmp_sccs
from Bio.SCOP import parse_domain
from Bio.SCOP import Scop
class ScopTests(unittest.TestCase):
def _compare_cla_lines(self, cla_line_1, cla_line_2):
"""Compare the two specified Cla lines for equality.
The order of the key-value pairs in the sixth field of the lines does
not matter. For more information, see
http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html.
"""
fields1 = cla_line_1.rstrip().split("\t")
fields2 = cla_line_2.rstrip().split("\t")
# compare the first five fields in a Cla line, which should be exactly
# the same
self.assertEqual(fields1[:5], fields2[:5])
# compare the hierarchy key-value pairs, which are unordered
self.assertCountEqual(fields1[5].split(","), fields2[5].split(","))
def testParse(self):
with open("./SCOP/dir.cla.scop.txt_test") as f:
cla = f.read()
with open("./SCOP/dir.des.scop.txt_test") as f:
des = f.read()
with open("./SCOP/dir.hie.scop.txt_test") as f:
hie = f.read()
scop = Scop(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
lines = zip(cla.rstrip().split("\n"), cla_out.getvalue().rstrip().split("\n"))
for expected_line, line in lines:
self._compare_cla_lines(expected_line, line)
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.assertIsNone(dom)
dom = scop.getDomainBySid("no such domain")
self.assertIsNone(dom)
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.assertIsInstance(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.assertIsNone(px)
# an sf has no px ascendent
px2 = sf.getAscendent("px")
self.assertIsNone(px2)
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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