def setUp(self):
self.buf = open('data/ProtDNA.psl').read()
self.buf = self.buf.replace("\r\n","\n")
thisdir = os.path.abspath(os.path.dirname(__file__))
def thisfile(name):
return os.path.join(thisdir, name)
self.srcDB = seqdb.SequenceFileDB(thisfile('data/test_prot.fa'))
self.destDB = seqdb.SequenceFileDB(thisfile('data/test_dna.fa'))
self.db = seqdb.SequenceFileDB(thisfile('data/translatedDB.fa'))
self.aln_type = 1 #protein-dna alignmet = 1, else - 0
self.matches, genome_names = blat_NLMSA.parse_blat(self.buf,
self.aln_type)
self.db = translationDB.get_translation_db(self.destDB)
alignment = cnestedlist.NLMSA('test', mode='memory', pairwiseMode=True,
bidirectional=False)
self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
aln_type = self.aln_type,
srcDB = self.srcDB,
destDB = self.db)
def test_parse_blat(self) :
matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.aln_type)
names_set = set(['gi|171854975|dbj|AB364477.1|',
'hbb1_mouse_RC',
'hbb1_mouse_RC_2',
'hbb1_mouse_RC_3',
'HBB0_PAGBO','HBB1_ANAMI',
'HBB1_CYGMA','HBB1_IGUIG',
'HBB1_MOUSE','HBB1_ONCMY',
'HBB1_PAGBO','HBB1_RAT',
'HBB1_SPHPU','HBB1_TAPTE',
'HBB1_TORMA','HBB1_TRICR',
'HBB1_UROHA','HBB1_VAREX',
'HBB1_XENBO','HBB1_XENLA',
'HBB1_XENTR','MYG_DIDMA',
'MYG_ELEMA','MYG_ERIEU',
'MYG_ESCGI','MYG_GALCR',
'PRCA_ANASP','PRCA_ANAVA'])
self.assertEqual(set(genome_names).difference(names_set),set())
blat_aln = matches[0] # Extracting the first alignment
qStart = getattr(blat_aln, "qStart")
tStart = getattr(blat_aln, "tStart")
qEnd = getattr(blat_aln, "qEnd")
tEnd = getattr(blat_aln, "tEnd")
qName = getattr(blat_aln, "qSeqName")
tName = getattr(blat_aln, "tSeqName")
orient = getattr(blat_aln, "orient")
blocks = getattr(blat_aln, "blocks")
last_ungapped = blocks[-1] # Extracting the last ungapped block
last_ungapped_qStart = getattr(last_ungapped, "qStart")
last_ungapped_tStart = getattr(last_ungapped, "tStart")
last_ungapped_qEnd = getattr(last_ungapped, "qEnd")
last_ungapped_tEnd = getattr(last_ungapped, "tEnd")
self.assertEqual(qStart, 20)
self.assertEqual(tStart, 63)
self.assertEqual(qEnd, 106)
self.assertEqual(tEnd, 321)
self.assertEqual(qName, 'HBB0_PAGBO')
self.assertEqual(tName, 'gi|171854975|dbj|AB364477.1|')
self.assertEqual(orient, '++')
self.assertEqual(len(blocks), 2)
self.assertEqual(last_ungapped_qStart, 81)
self.assertEqual(last_ungapped_tStart, 246)
self.assertEqual(last_ungapped_qEnd, 81+25)
self.assertEqual(last_ungapped_tEnd, 246+3*25)
def setUp(self):
self.buf = open('data/output.psl').read()
self.buf = self.buf.replace("\r\n","\n")
thisdir = os.path.abspath(os.path.dirname(__file__))
self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
'data/test_genomes.fna'))
self.aln_type = 0 #if protein-dna-1,else-0
matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.aln_type)
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
seqDB=self.db)
def setUp(self):
self.buf = open('data/output.psl').read()
self.buf = self.buf.replace("\r\n","\n")
thisdir = os.path.abspath(os.path.dirname(__file__))
def thisfile(name):
return os.path.join(thisdir, name)
self.srcDB = seqdb.SequenceFileDB(thisfile('data/test_genomes.fna'))
self.destDB = seqdb.SequenceFileDB(thisfile('data/test_genomes.fna'))
self.protDNAaln = False #if protein-dna alignment - True,else- False
matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.protDNAaln)
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.srcDB,
use_virtual_lpo=True)
#alignment = cnestedlist.NLMSA('test', mode='memory', pairwiseMode=True,
#bidirectional=False)????????
self.temp_nlmsa = blat_NLMSA.create_NLMSA_blat(self.buf, alignment,
self.srcDB, self.destDB,
self.protDNAaln)
def test_parse_blat(self) :
matches, genome_names = blat_NLMSA.parse_blat(self.buf, self.protDNAaln)
self.assertEqual(set(genome_names), set(['testgenome1', 'testgenome2',
'testgenome3', 'testgenome4']))
blat_aln = matches[-1]
qStart = getattr(blat_aln, "qStart")
tStart = getattr(blat_aln, "tStart")
qEnd = getattr(blat_aln, "qEnd")
tEnd = getattr(blat_aln, "tEnd")
qName = getattr(blat_aln, "qSeqName")
tName = getattr(blat_aln, "tSeqName")
orient = getattr(blat_aln, "orient")
blocks = getattr(blat_aln, "blocks")
last_ungapped = blocks[-1]
last_ungapped_qStart = getattr(last_ungapped, "qStart")
last_ungapped_tStart = getattr(last_ungapped, "tStart")
last_ungapped_qEnd = getattr(last_ungapped, "qEnd")
last_ungapped_tEnd = getattr(last_ungapped, "tEnd")
self.assertEqual(qStart, 64)
self.assertEqual(tStart, 64)
self.assertEqual(qEnd, 420)
self.assertEqual(tEnd, 350)
self.assertEqual(qName, 'testgenome4')
self.assertEqual(tName, 'testgenome1')
self.assertEqual(orient, '++')
self.assertEqual(len(blocks), 2)
self.assertEqual(last_ungapped_qStart, 351)
self.assertEqual(last_ungapped_tStart, 281)
self.assertEqual(last_ungapped_qEnd, 351+69)
self.assertEqual(last_ungapped_tEnd, 281+69)