def bootstrap(self, mapping_data, nboot, nsamples=-1, algorithm='rnastructure', bonus2d=False, replacement=False):
print 'Starting bootstrap...'
print 'Folding RNA with complete data'
if bonus2d:
mappind_data = array(mapping_data)
if nsamples < 0:
nsamples = len(self.sequence)
full_bps = secondary_structure.fold(self.sequence, algorithm=algorithm, mapping_data=mapping_data, bonus2d=bonus2d)[0].base_pairs()
bpdict = dict([(bp, 0) for bp in full_bps])
for i in range(nboot):
print 'Doing bootstrap iteration %s' % i
if bonus2d:
grid = indices(mapping_data.shape)
all_indices = zip(grid[0].ravel(), grid[1].ravel())
sampled_indices = [choice(all_indices) for x in xrange(len(all_indices))]
md = zeros(mapping_data.shape)
for j,k in sampled_indices:
md[j,k] += mapping_data[j,k]
else:
md = mapping_data.sample(nsamples, replacement=replacement)
bps = secondary_structure.fold(self.sequence, algorithm=algorithm, mapping_data=md, bonus2d=bonus2d)[0].base_pairs()
for bp in bps:
if bp in bpdict:
bpdict[bp] += 1
else:
bpdict[bp] = 1
for bp in bpdict:
bpdict[bp] *= 100./nboot
return bpdict
import rna
import settings
import secondary_structure
import view
import mapping
s = 'UGCGCUUUUUUUUGCGCUUUUUUUUGCGCU'
molecule = rna.RNA(s)
data = mapping.MappingData(data=[0,0], seqpos=[2,26])
data2 = mapping.MappingData(data=[0,0], seqpos=[3,26])
structures = secondary_structure.fold(molecule.sequence, mapping_data=data,algorithm='rnastructure')
ba = molecule.bootstrap(data, 5, nsamples=1, replacement=True)
for b in ba:
ba[b] = str(ba[b]) +'%'
applet = view.VARNA(sequences=[molecule.sequence], structures=structures, mapping_data=[data])
html = applet.render(base_annotations=[ba], annotation_by_helix=True, \
helix_function=(lambda x, y: max(x,y)))
f = open('test.html', 'w')
f.write(html)
f.close()
import rna
import settings
import secondary_structure
import view
import mapping
s = 'UGCGCUUUUUUUUGCGCUUUUUUUUGCGCU'
molecule = rna.RNA(s)
data = mapping.MappingData(data=[0, 0], seqpos=[2, 26])
data2 = mapping.MappingData(data=[0, 0], seqpos=[3, 26])
structures = secondary_structure.fold(molecule.sequence,
mapping_data=data,
algorithm='rnastructure')
ba = molecule.bootstrap(data, 5, nsamples=1, replacement=True)
for b in ba:
ba[b] = str(ba[b]) + '%'
applet = view.VARNA(sequences=[molecule.sequence],
structures=structures,
mapping_data=[data])
html = applet.render(base_annotations=[ba], annotation_by_helix=True, \
helix_function=(lambda x, y: max(x,y)))
f = open('test.html', 'w')
f.write(html)
f.close()