def ap1_included(motifs): ap1 = motif_from_consensus("TGASTCA") mc = MotifComparer() match = mc.get_closest_match(ap1, motifs, metric="seqcor") print(match) if match["TGASTCA"][1][0] >= 0.75: return True return False
def ap1_included(self, motifs): ap1 = motif_from_consensus("TGASTCA") mc = MotifComparer() for motif in motifs: match = mc.get_closest_match(ap1, motif) if match["TGASTCA"][1][3] < 1e-6: return True return False
def ap1_included(self, motifs): #if len(motifs) == 0: # return False ap1 = motif_from_consensus("TGASTCA") mc = MotifComparer() match = mc.get_closest_match(ap1, motifs, metric="seqcor") print(match) if match["TGASTCA"][1][0] >= 0.8: return True return False
def test1_denovo(self): """ de novo motif prediction """ gimme_motifs( "test/data/denovo/input.fa", self.outdir, params={ "tools": "BioProspector,Homer,MDmodule", "fraction": 0.5, "background": "random", "genome": "test/data/background/genome.fa", }, filter_significant=True, cluster=True, ) fnames = [ "gimme.denovo.pfm", "gimme.denovo.html", "gimme.clustereds.html", "params.txt", "stats.random.txt", ] with open(os.path.join(self.outdir, "gimmemotifs.log")) as f: log = f.read() self.assertIn("clustering", log) # Check if all output files are there for fname in fnames: self.assertTrue(os.path.exists(os.path.join(self.outdir, fname))) # Check if correct motif is predicted with open(os.path.join(self.outdir, "gimme.denovo.pfm")) as f: predicted_motifs = read_motifs(f) ap1 = motif_from_consensus("TGASTCA") mc = MotifComparer() ap1_predicted = False for motif in predicted_motifs: match = mc.get_closest_match(ap1, motif) if match["TGASTCA"][1][3] < 1e-5: ap1_predicted = True break self.assertTrue(ap1_predicted)
def test1_denovo(self): """ de novo motif prediction """ gimme_motifs("test/data/denovo/input.fa", self.outdir, params={ "tools":"BioProspector,Homer,MDmodule", "fraction":0.5, "background":"random" }, filter_significant=True, cluster=True) fnames = ["motifs.pwm", "motif_report.html", "cluster_report.html", "params.txt", "stats.random.txt"] with open(os.path.join(self.outdir, 'gimmemotifs.log')) as f: log = f.read() self.assertIn("clustering", log) # Check if all output files are there for fname in fnames: self.assertTrue(os.path.exists(os.path.join(self.outdir, fname))) # Check if correct motif is predicted with open(os.path.join(self.outdir, "motifs.pwm")) as f: predicted_motifs = read_motifs(f) ap1 = motif_from_consensus("TGASTCA") mc = MotifComparer() ap1_predicted = False for motif in predicted_motifs: match = mc.get_closest_match(ap1, motif) if match["TGASTCA"][1][3] < 1e-5: ap1_predicted = True break self.assertTrue(ap1_predicted)