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 test_create_default(self):
ms = MotifSet()
self.assertEqual(
len(ms),
0,
msg="motif dictionary must be empty by default (no preload)")
motif_list = ms.get_motif_list(1.0, 0.0001)
self.assertEqual(len(motif_list), 0)
def test_create_empty(self):
ms = MotifSet(preload_motifs=None)
self.assertEqual(len(ms), 0, msg="motif dictionary must be empty")
motif_list = ms.get_motif_list(1.0, 0.0001)
self.assertEqual(len(motif_list), 0)
def test_create_default(self):
ms = MotifSet()
self.assertEqual(len(ms), 0, msg="motif dictionary must be empty by default (no preload)")
motif_list = ms.get_motif_list(1.0, 0.0001)
self.assertEqual(len(motif_list), 0)