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)