Python gff_enrichment Examples

Example #1

File: test_pwmscan.py Project: PanosFirmpas/gimmemotifs

 def test3_gff_enrichment(self):
     """ Test gff_enrichment """
     self.motif.pwm_scan_to_gff(self.random, self.random_gff)
     gff_enrichment(self.prom_gff, self.random_gff, 316, 3160, self.tmp)
     f = open(self.tmp)
     f.readline() # Header
     vals = f.readline().strip().split("\t")
     self.assertEquals(vals[0], "TATA-box")
     self.assertLess(float(vals[2]), 1e-60)
     self.assertGreater(float(vals[5]), 1.5)

Example #2

 def test3_gff_enrichment(self):
     """ Test gff_enrichment """
     self.motif.pwm_scan_to_gff(self.random, self.random_gff)
     gff_enrichment(self.prom_gff, self.random_gff, 316, 3160, self.tmp)
     f = open(self.tmp)
     f.readline() # Header
     vals = f.readline().strip().split("\t")
     self.assertEquals(vals[0], "TATA-box")
     self.assertLess(float(vals[2]), 1e-60)
     self.assertGreater(float(vals[5]), 1.5)

Example #3

File: test_pwmscan.py Project: astatham/gimmemotifs

	def test3_gff_enrichment(self):
		""" Test gff_enrichment """
		self.motif.pwm_scan_to_gff(self.random, self.random_gff)
		gff_enrichment(self.prom_gff, self.random_gff, 316, 3160, self.tmp)
		self.assertEquals(open(self.enrichment).read(), open(self.tmp).read())

Example #4

 def test3_gff_enrichment(self):
     """ Test gff_enrichment """
     self.motif.pwm_scan_to_gff(self.random, self.random_gff)
     gff_enrichment(self.prom_gff, self.random_gff, 316, 3160, self.tmp)
     self.assertEquals(open(self.enrichment).read(), open(self.tmp).read())