def setUp(self):
self.buf = open('output').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,
'test_genomes.fna'))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(self.buf,
self.db, alignment)
def setUp(self):
self.buf = open('output').read()
thisdir = os.path.abspath(os.path.dirname(__file__))
self.db = seqdb.SequenceFileDB(os.path.join(thisdir,
'test_genomes.fna'))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
genomes_dict = {}
for genome in genome_names:
genomes_dict[genome] = self.db[genome]
alignment = cnestedlist.NLMSA('test', mode='memory', seqDict=self.db,
use_virtual_lpo=True)
alignment += genomes_dict[genome_names[0]]
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(os.path.join(thisdir, 'output'),
self.db, alignment)
def setUp(self):
self.buf = open("output").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.db = seqdb.SequenceFileDB(thisfile("test_genomes.fna"))
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
alignment = cnestedlist.NLMSA("test", mode="memory", seqDict=self.db, use_virtual_lpo=True)
self.temp_nlmsa = blastz_NLMSA.create_NLMSA_blastz(self.buf, self.db, alignment)
def test_parse_blastz(self):
matches, genome_names = blastz_NLMSA.parse_blastz(self.buf)
self.assertEqual(set(genome_names), set(["testgenome1", "testgenome2"]))
blastz_aln = matches[-1]
score = getattr(blastz_aln, "score")
start_top = getattr(blastz_aln, "start_top")
start_bot = getattr(blastz_aln, "start_bot")
end_top = getattr(blastz_aln, "end_top")
end_bot = getattr(blastz_aln, "end_bot")
sequence_name1 = getattr(blastz_aln, "sequence_name1")
sequence_name2 = getattr(blastz_aln, "sequence_name2")
orient = getattr(blastz_aln, "orient")
blocks = getattr(blastz_aln, "blocks")
last_ungapped = blocks[-1]
last_ungapped_start_top = getattr(last_ungapped, "start_top")
last_ungapped_start_bot = getattr(last_ungapped, "start_bot")
last_ungapped_end_top = getattr(last_ungapped, "end_top")
last_ungapped_end_bot = getattr(last_ungapped, "end_bot")
last_ungapped_ident = getattr(last_ungapped, "ident")
self.assertEqual(score, 74457)
self.assertEqual(start_top, 40)
self.assertEqual(start_bot, 41)
self.assertEqual(end_top, 1120)
self.assertEqual(end_bot, 1120)
self.assertEqual(sequence_name1, "testgenome1")
self.assertEqual(sequence_name2, "testgenome2")
self.assertEqual(orient, 1)
self.assertEqual(len(blocks), 4)
self.assertEqual(last_ungapped_start_top, 302)
self.assertEqual(last_ungapped_start_bot, 302)
self.assertEqual(last_ungapped_end_top, 1120)
self.assertEqual(last_ungapped_end_bot, 1120)
self.assertEqual(last_ungapped_ident, 84)