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)
