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"""Tests for parsing Compass output.
"""
import os
import sys
import unittest
from Bio import Compass
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 'test'
tests = [CompassTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class CompassTest(unittest.TestCase):
def setUp(self):
file_dir = os.path.join("Compass")
self.test_files = [
os.path.join(file_dir, "comtest1"),
os.path.join(file_dir, "comtest2"),
os.path.join(file_dir, "comtest3")]
def testCompassScanAndConsume(self):
cons = Compass._Consumer()
scan = Compass._Scanner()
scan.feed(open(self.test_files[0]), cons)
com_record = cons.data
self.assertEquals("60456.blo.gz.aln", com_record.query)
self.assertEquals("60456.blo.gz.aln", com_record.hit)
self.assertEquals(0.5, com_record.gap_threshold)
self.assertEquals(388, com_record.query_length)
self.assertEquals(386, com_record.query_filtered_length)
self.assertEquals(388, com_record.hit_length)
self.assertEquals(386, com_record.hit_filtered_length)
self.assertEquals(399, com_record.query_nseqs)
self.assertEquals(12.972, com_record.query_neffseqs)
self.assertEquals(399, com_record.hit_nseqs)
self.assertEquals(12.972, com_record.hit_neffseqs)
self.assertEquals(2759, com_record.sw_score)
self.assertEquals(float("0.00e+00"), com_record.evalue)
def testCompassParser(self):
parser = Compass.RecordParser()
com_record = parser.parse(open(self.test_files[0]))
self.assertEquals("60456.blo.gz.aln", com_record.query)
def testCompassIteratorEasy(self):
it = Compass.Iterator(open(self.test_files[0]))
com_record = it.next()
self.assertEquals("60456.blo.gz.aln", com_record.query)
com_record = it.next()
self.assertEquals(None, com_record)
pass
def testCompassIteratorHard(self):
it = Compass.Iterator(open(self.test_files[1]))
com_record = it.next()
self.assertEquals("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEquals(float('1.01e+03'), com_record.evalue)
com_record = it.next()
self.assertEquals("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEquals(float('1.01e+03'), com_record.evalue)
com_record = it.next()
self.assertEquals("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEquals(float('5.75e+02'), com_record.evalue)
def testAlignmentParsingOne(self):
it = Compass.Iterator(open(self.test_files[1]))
com_record = it.next()
self.assertEquals(178, com_record.query_start)
self.assertEquals("KKDLEEIAD", com_record.query_aln)
self.assertEquals(9, com_record.hit_start)
self.assertEquals("QAAVQAVTA", com_record.hit_aln)
self.assertEquals("++ ++++++", com_record.positives)
com_record = it.next()
com_record = it.next()
self.assertEquals(371, com_record.query_start)
self.assertEquals("LEEAMDRMER~~~V", com_record.query_aln)
self.assertEquals(76, com_record.hit_start)
self.assertEquals("LQNFIDQLDNpddL", com_record.hit_aln)
self.assertEquals("+ ++++ + + +", com_record.positives)
def testAlignmentParsingTwo(self):
it = Compass.Iterator(open(self.test_files[0]))
com_record = it.next()
self.assertEquals(2, com_record.query_start)
self.assertEquals(2, com_record.hit_start)
self.assertEquals("LKERKL", com_record.hit_aln[-6:])
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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