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test_SCOP_Cla.py
# 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




00018 class ClaTests(unittest.TestCase):

    def setUp(self):
        self.filename = './SCOP/dir.cla.scop.txt_test'

00023     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()
    
00035     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.iteritems():
                    self.assertEqual(actual_value, expected_hierarchy[key])
        finally:
            f.close()        

00060     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)

00065     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})

00083     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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