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_translation_db_in_results_of_db_search(self):
"""
Test that the NLMSA in a BlastxMapping properly picks up the
translationDB from the query sequence dict.
"""
if not testutil.blast_enabled():
raise SkipTest("no BLAST installed")
blastmap = blast.BlastxMapping(self.prot, verbose=False)
results = blastmap(queryDB=self.dna)
tdb = translationDB.get_translation_db(self.dna)
assert tdb.annodb in results.seqDict.dicts
def test_translation_db_in_results_of_seq_search(self):
"""
Test that the NLMSA in a BlastxMapping properly picks up the
translationDB from a single input sequence.
"""
if not testutil.blast_enabled():
raise SkipTest("no BLAST installed")
blastmap = blast.BlastxMapping(self.prot, verbose=False)
query_seq = self.dna["gi|171854975|dbj|AB364477.1|"]
results = blastmap(seq=query_seq)
tdb = translationDB.get_translation_db(self.dna)
assert tdb.annodb in results.seqDict.dicts
def test_translated_seqs_in_results(self):
"""
Only NLMSASlices for the query sequence should show up in
BlastxMapping.__getitem__, right?
"""
if not testutil.blast_enabled():
raise SkipTest("no BLAST installed")
blastmap = blast.BlastxMapping(self.prot, verbose=False)
query_seq = self.dna["gi|171854975|dbj|AB364477.1|"]
results = blastmap[query_seq]
tdb = translationDB.get_translation_db(self.dna)
annodb = tdb.annodb
for slice in results:
assert slice.seq.id in annodb, "%s not in annodb!" % slice.seq.id
def setUp(self):
hbb1_mouse = testutil.datafile('hbb1_mouse.fa')
self.dna = seqdb.SequenceFileDB(hbb1_mouse)
self.tdb = translationDB.get_translation_db(self.dna)
def setUp(self):
hbb1_mouse = testutil.datafile('hbb1_mouse.fa')
self.dna = seqdb.SequenceFileDB(hbb1_mouse)
self.tdb = translationDB.get_translation_db(self.dna)
