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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 Cla."""
import unittest
from Bio.SCOP import Cla
class ClaTests(unittest.TestCase):
def setUp(self):
self.filename = "./SCOP/dir.cla.scop.txt_test"
def testParse(self):
"""Test if all records in a CLA file are being read."""
count = 0
with open(self.filename) as f:
records = Cla.parse(f)
for record in records:
count += 1
self.assertEqual(count, 14)
def testStr(self):
"""Test if we can convert each record to a string correctly."""
with open(self.filename) as f:
for line in f:
record = Cla.Record(line)
# The SCOP Classification file format which can be found at
# http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html states
# that the list of classification hierarchy key-value pairs is
# unordered, therefore we need only check that they are all
# there, NOT that they are in the same order.
# End of line is platform dependent. Strip it off
expected_hierarchy = line.rstrip().split("\t")[5].split(",")
expected_hierarchy = dict(
pair.split("=") for pair in expected_hierarchy
)
actual_hierarchy = str(record).rstrip().split("\t")[5].split(",")
actual_hierarchy = dict(pair.split("=") for pair in actual_hierarchy)
self.assertEqual(len(actual_hierarchy), len(expected_hierarchy))
for key, actual_value in actual_hierarchy.items():
self.assertEqual(actual_value, expected_hierarchy[key])
def testError(self):
"""Test if a corrupt record raises the appropriate exception."""
corruptRec = "49268\tsp\tb.1.2.1\t-\n"
self.assertRaises(ValueError, Cla.Record, corruptRec)
def testRecord(self):
"""Test one record in detail."""
recLine = "d1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953"
record = Cla.Record(recLine)
self.assertEqual(record.sid, "d1dan.1")
self.assertEqual(record.residues.pdbid, "1dan")
self.assertEqual(record.residues.fragments, (("T", "", ""), ("U", "91", "106")))
self.assertEqual(record.sccs, "b.1.2.1")
self.assertEqual(record.sunid, 21953)
self.assertEqual(
record.hierarchy,
{
"cl": 48724,
"cf": 48725,
"sf": 49265,
"fa": 49266,
"dm": 49267,
"sp": 49268,
"px": 21953,
},
)
def testIndex(self):
"""Test CLA file indexing."""
index = Cla.Index(self.filename)
self.assertEqual(len(index), 14)
self.assertIn("d4hbia_", index)
rec = index["d1hbia_"]
self.assertEqual(rec.sunid, 14996)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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