def testCompassScanAndConsume(self):
com_record = Compass.read(open(self.test_files[0]))
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertEqual("60456.blo.gz.aln", com_record.hit)
self.assertEqual(0.5, com_record.gap_threshold)
self.assertEqual(388, com_record.query_length)
self.assertEqual(386, com_record.query_filtered_length)
self.assertEqual(388, com_record.hit_length)
self.assertEqual(386, com_record.hit_filtered_length)
self.assertEqual(399, com_record.query_nseqs)
self.assertEqual(12.972, com_record.query_neffseqs)
self.assertEqual(399, com_record.hit_nseqs)
self.assertEqual(12.972, com_record.hit_neffseqs)
self.assertEqual(2759, com_record.sw_score)
self.assertEqual(float("0.00e+00"), com_record.evalue)
def testCompassScanAndConsume(self):
with open(self.test_files[0]) as handle:
com_record = Compass.read(handle)
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertEqual("60456.blo.gz.aln", com_record.hit)
self.assertEqual(0.5, com_record.gap_threshold)
self.assertEqual(388, com_record.query_length)
self.assertEqual(386, com_record.query_filtered_length)
self.assertEqual(388, com_record.hit_length)
self.assertEqual(386, com_record.hit_filtered_length)
self.assertEqual(399, com_record.query_nseqs)
self.assertEqual(12.972, com_record.query_neffseqs)
self.assertEqual(399, com_record.hit_nseqs)
self.assertEqual(12.972, com_record.hit_neffseqs)
self.assertEqual(2759, com_record.sw_score)
self.assertEqual(float("0.00e+00"), com_record.evalue)
def testCompassParser(self):
com_record = Compass.read(open(self.test_files[0]))
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
with open(self.test_files[0]) as handle:
com_record = Compass.read(handle)
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
