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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"""
f = open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count += 1
self.assertEqual(count, 14)
finally:
f.close()
def testStr(self):
"""Test if we can convert each record to a string correctly"""
f = open(self.filename)
try:
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])
finally:
f.close()
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.assertTrue('d4hbia_' in 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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