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91 lines
3.3 KiB
Python
91 lines
3.3 KiB
Python
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
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# Modifications Copyright 2010 Jeffrey Finkelstein. All rights reserved.
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#
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Unit test for Cla."""
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import unittest
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from Bio.SCOP import Cla
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class ClaTests(unittest.TestCase):
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def setUp(self):
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self.filename = "./SCOP/dir.cla.scop.txt_test"
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def testParse(self):
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"""Test if all records in a CLA file are being read."""
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count = 0
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with open(self.filename) as f:
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records = Cla.parse(f)
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for record in records:
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count += 1
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self.assertEqual(count, 14)
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def testStr(self):
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"""Test if we can convert each record to a string correctly."""
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with open(self.filename) as f:
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for line in f:
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record = Cla.Record(line)
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# The SCOP Classification file format which can be found at
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# http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html states
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# that the list of classification hierarchy key-value pairs is
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# unordered, therefore we need only check that they are all
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# there, NOT that they are in the same order.
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# End of line is platform dependent. Strip it off
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expected_hierarchy = line.rstrip().split("\t")[5].split(",")
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expected_hierarchy = dict(
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pair.split("=") for pair in expected_hierarchy
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)
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actual_hierarchy = str(record).rstrip().split("\t")[5].split(",")
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actual_hierarchy = dict(pair.split("=") for pair in actual_hierarchy)
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self.assertEqual(len(actual_hierarchy), len(expected_hierarchy))
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for key, actual_value in actual_hierarchy.items():
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self.assertEqual(actual_value, expected_hierarchy[key])
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def testError(self):
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"""Test if a corrupt record raises the appropriate exception."""
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corruptRec = "49268\tsp\tb.1.2.1\t-\n"
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self.assertRaises(ValueError, Cla.Record, corruptRec)
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def testRecord(self):
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"""Test one record in detail."""
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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"
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record = Cla.Record(recLine)
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self.assertEqual(record.sid, "d1dan.1")
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self.assertEqual(record.residues.pdbid, "1dan")
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self.assertEqual(record.residues.fragments, (("T", "", ""), ("U", "91", "106")))
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self.assertEqual(record.sccs, "b.1.2.1")
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self.assertEqual(record.sunid, 21953)
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self.assertEqual(
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record.hierarchy,
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{
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"cl": 48724,
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"cf": 48725,
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"sf": 49265,
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"fa": 49266,
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"dm": 49267,
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"sp": 49268,
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"px": 21953,
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},
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)
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def testIndex(self):
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"""Test CLA file indexing."""
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index = Cla.Index(self.filename)
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self.assertEqual(len(index), 14)
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self.assertIn("d4hbia_", index)
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rec = index["d1hbia_"]
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self.assertEqual(rec.sunid, 14996)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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