コード例 #1
0
ファイル: blastz_NLMSA_test.py プロジェクト: ctb/pygr-align
    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)
コード例 #2
0
    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)
コード例 #3
0
    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)
コード例 #4
0
    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)