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)