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:])
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)