def test_pad():
a = np.zeros((20, 4))
a[12] = 1
a_short = a[5:15]
assert a_short[7][0] == 1
assert a[12][0] == 1
assert a[13][0] == 0
p = Pattern("test",
a_short,
dict(t=a_short),
dict(t=a_short),
dict(t=a))
assert np.all(p.profile['t'] == a)
assert p.len_profile() == 20
assert p.pad(10).len_profile() == 20
assert len(p.pad(10)) == 10
assert len(p.pad(10)) == 10
assert p.shift(-2).profile['t'][10][0] == 1
assert p.shift(-2).contrib['t'][5][0] == 1
pnew = p.shift(1).rc().shift(1).rc()
assert np.allclose(p.seq, pnew.seq)
assert np.allclose(p.contrib['t'], pnew.contrib['t'])
assert np.allclose(p.profile['t'], pnew.profile['t'])
def create_patterns(motif_seqs):
patterns = [
Pattern(seq=encodeDNA([s])[0],
contrib=dict(a=encodeDNA([s])[0]),
hyp_contrib=dict(a=encodeDNA([s])[0]),
name=str(i)) for i, s in enumerate(motif_seqs)
]
aligned_patterns = [
p.align(patterns[0], pad_value=np.array([0.25] * 4)) for p in patterns
]
return patterns, aligned_patterns
def _extract(cls, seqlet, seq, hyp_contrib, profiles, profile_width=None):
"""Extract all the values using the seqlet
"""
from basepair.modisco.core import Pattern
ex_hyp_contrib = {task: seqlet.extract(arr)
for task, arr in hyp_contrib.items()}
ex_seq = seqlet.extract(seq)
# TODO - implement this to work also for the out-of-core case efficiently
wide_seqlet = seqlet.resize(profile_width)
return Pattern(name=seqlet.name,
seq=ex_seq,
contrib={task: arr * ex_seq for task, arr in ex_hyp_contrib.items()},
hyp_contrib=ex_hyp_contrib,
profile={task: wide_seqlet.extract(arr)
for task, arr in profiles.items()},
attrs=dict()
)
def dont_test_parse_hdf4():
from basepair.modisco.results import ModiscoResult
mr = ModiscoResult("/s/project/avsec/basepair/modisco/modisco.h5")
mr.open()
mr.f.ls()
metacluster = "metacluster_0"
pattern = "pattern_0"
pattern_grp = mr.get_pattern_grp(metacluster, pattern)
p = Pattern.from_hdf5_grp(pattern_grp, "m0_p0")
pt = p.trim_seq_ic(0.08)
assert len(pt) == len(pt.contrib['Klf4'])
p = mr.get_pattern("metacluster_0/pattern_0")
import matplotlib.pyplot as plt
p.plot(kind='all')
p.plot(kind=['seq', 'contrib/Klf4'])
p.plot(kind='seq')
plt.show()
mr.plot_pattern("metacluster_0/pattern_0", kind=['seq', 'contrib/Klf4'])
def test_pattern():
p = Pattern("test",
np.random.randn(10, 4),
dict(t=np.random.randn(10, 4)),
dict(t=np.random.randn(10, 4)))
assert p.tasks() == ['t']
print(p)
p.get_consensus()
p.seq = np.abs(p.seq)
p.get_seq_ic()
p.copy()
p.copy()
p.rc()
len(p)
with raises(Exception):
p = Pattern("test",
np.random.randn(10, 4),
dict(t=np.random.randn(10, 4)),
dict(t=np.random.randn(11, 4)))
with raises(Exception):
p = Pattern("test",
np.random.randn(10, 4),
[5] * 10,
np.random.randn(10, 4))
def get_pattern(self, pattern):
"""Get the pattern name
"""
from basepair.modisco.core import Pattern
return Pattern.from_hdf5_grp(self.get_pattern_grp(*pattern.split("/")),
pattern)