class MatchTest(unittest.TestCase):
def setUp(self):
# the genome must be available
# TODO: we could make this test pure by manually using the sequence corresponding to the input region
self.genome_data = GenomeData("hg19")
self.genome_file = Fastafile(self.genome_data.get_genome())
def test_match_multiple(self):
dirname = os.path.dirname(__file__)
jasp_dir = "../../data/motifs/jaspar_vertebrates/"
scanner = scan.Scanner(7)
pssm_list = []
thresholds = []
motif = Motif(os.path.join(dirname, jasp_dir, "MA0139.1.CTCF.pwm"), 1,
0.0001, None)
thresholds.append(motif.threshold)
thresholds.append(motif.threshold_rc)
pssm_list.append(motif.pssm)
pssm_list.append(motif.pssm_rc)
bg = tools.flat_bg(4)
scanner.set_motifs(pssm_list, bg, thresholds)
genomic_region = GenomicRegion("chr1", 710000, 715000)
# Reading sequence associated to genomic_region
sequence = str(
self.genome_file.fetch(genomic_region.chrom,
genomic_region.initial,
genomic_region.final))
grs = match_multiple(scanner, [motif], sequence, genomic_region)
self.assertSequenceEqual(grs.sequences, [
GenomicRegion(
"chr1", 714270, 714289, name="MA0139.1.CTCF", orientation="+"),
GenomicRegion(
"chr1", 714180, 714199, name="MA0139.1.CTCF", orientation="-")
])
class MatchTest(unittest.TestCase):
def setUp(self):
# the genome must be available
# TODO: we could make this test pure by manually using the sequence corresponding to the input region
self.genome_data = GenomeData("hg19")
self.genome_data.genome = os.path.join(os.path.dirname(__file__), "hg19_chr1_710000_715000.fa")
self.genome_file = Fastafile(self.genome_data.get_genome())
def test_match_multiple(self):
ms = MotifSet(preload_motifs="default")
ms = ms.filter({'database': ["jaspar_vertebrates"], 'name': ["MA0139.1.CTCF"]}, search="inexact")
self.assertEqual(len(ms), 1)
motif = ms.get_motif_list(1, 0.0001)[0]
scanner = scan.Scanner(7)
pssm_list, thresholds = [], []
thresholds.append(motif.threshold)
thresholds.append(motif.threshold)
pssm_list.append(motif.pssm)
pssm_list.append(motif.pssm_rc)
bg = tools.flat_bg(4)
scanner.set_motifs(pssm_list, bg, thresholds)
genomic_region = GenomicRegion("chr1", 0, 5022)
# Reading sequence associated to genomic_region
sequence = str(self.genome_file.fetch(genomic_region.chrom, genomic_region.initial, genomic_region.final))
grs = match_multiple(scanner, [motif], sequence, genomic_region)
self.assertSequenceEqual(grs.sequences,
[GenomicRegion("chr1", 4270, 4289, name="MA0139.1.CTCF", orientation="+"),
GenomicRegion("chr1", 4180, 4199, name="MA0139.1.CTCF", orientation="-")])
def setUp(self):
# the genome must be available
# TODO: we could make this test pure by manually using the sequence corresponding to the input region
self.genome_data = GenomeData("hg19")
self.genome_data.genome = os.path.join(os.path.dirname(__file__), "hg19_chr1_710000_715000.fa")
self.genome_file = Fastafile(self.genome_data.get_genome())
def setUp(self):
# the genome must be available
# TODO: we could make this test pure by manually using the sequence corresponding to the input region
self.genome_data = GenomeData("hg19")
self.genome_file = Fastafile(self.genome_data.get_genome())