def testPow(self):
x = interval.Interval([-1, 2])
z = x ** 3
self.assertEqual(z.x, [-1,8])
z = x ** 4
self.assertEqual(z.x, [0,16])
def testSin(self):
x = interval.Interval([-math.pi/6, 2])
z = interval.sin(x)
for i in range(len(z.x)):
self.assertAlmostEqual(z.x[i], [-0.5,1][i])
def testAdd(self):
x = interval.Interval([-1, 2])
y = interval.Interval([1, 2])
z = x + y
self.assertEqual(z.x, [0, 4])
def testSub(self):
x = interval.Interval([-1, 2])
y = interval.Interval([1, 2])
z = y - x
self.assertEqual(z.x, [-1, 3])
intronic[chrom].difference_update( pc_exons[chrom] )
intronic[chrom].difference_update( other_ens[chrom] )
UTRs = pc_exons
for chrom in chroms:
UTRs[chrom].difference_update( CDS[chrom] )
old_idi_id=""; cuff_coords=interval(); firsttime=True; cuff_present=False
for line in cuff:
la = line.rstrip('\n').split('\t')
idi_id = la[8].split('";')[0].split('"')[1]
if (not firsttime) and (not idi_id == old_idi_id):
old_idi_id = idi_id
if ens_here and cuff_present:
cuff_exons[chrom].update( cuff_coords )
cuff_introns_here = interval.IntervalSet([interval.Interval( cuff_exons[chrom].lower_bound(), cuff_exons[chrom].upper_bound() )])
cuff_introns_here.difference_update( cuff_exons[chrom] )
cuff_introns[chrom].update(cuff_introns_here)
cuff_coords=interval.IntervalSet([])
ens_here = False
cuff_present = False
firsttime = False
chrom = la[0]
if la[1] == "Cufflinks":
cuff_coords.add( interval.Interval(min( map(int,la[3:5]) ), max( map(int,la[3:5]) )) )
cuff_present=True
else:
ens_here = True
if ens_here and cuff_present: # accounting for the final iteration
cuff_exons[chrom].update( cuff_coords )
cuff_introns_here = interval.IntervalSet([interval.Interval( cuff_exons[chrom].lower_bound(), cuff_exons[chrom].upper_bound() )])
'ab1': binary.Ab1(), 'axt': sequence.Axt(), 'bam': binary.Bam(), 'bed': interval.Bed(), 'binseq.zip': binary.Binseq(), 'blastxml': xml.BlastXml(), 'coverage': coverage.LastzCoverage(), 'customtrack': interval.CustomTrack(), 'csfasta': sequence.csFasta(), 'fasta': sequence.Fasta(), 'fastq': sequence.Fastq(), 'fastqsanger': sequence.FastqSanger(), 'gff': interval.Gff(), 'gff3': interval.Gff3(), 'genetrack': tracks.GeneTrack(), 'interval': interval.Interval(), 'laj': images.Laj(), 'lav': sequence.Lav(), 'maf': sequence.Maf(), 'pileup': tabular.Pileup(), 'qualsolid': qualityscore.QualityScoreSOLiD(), 'qualsolexa': qualityscore.QualityScoreSolexa(), 'qual454': qualityscore.QualityScore454(), 'sam': tabular.Sam(), 'scf': binary.Scf(), 'sff': binary.Sff(), 'tabular': tabular.Tabular(), 'taxonomy': tabular.Taxonomy(), 'txt': data.Text(), 'txtseq.zip': data.Txtseq(), 'wig': interval.Wiggle()
def __init__(self, value, x):
Expr.__init__(self)
self.L = 0
self.value = value
self.range = interval.Interval([value, value])
self.x = x
def getbnd(self):
hl = 0.5 * (self.x[1] - self.x[0])
bnd = interval.Interval(
[self.value - self.L * hl, self.value + self.L * hl])
self.range.intersec(bnd)
return bnd
def pijav_bnb(problem, eps, solinfo, maxsteps):
"""
Pijavsky method enhanced with slopes
:param problem: problem to solver
:param eps: tolerance
:param solinfo: obtained solution
:return: actual steps performed
"""
class Sub:
def __init__(self, s1, s2, ival):
self.s1 = s1
self.s2 = s2
self.ival = ival
a = ival[0]
b = ival[1]
La = s1.S[0]
Lb = s2.S[1]
va = s1.value
vb = s2.value
self.c = (vb - va + La * a - Lb * b) / (La - Lb)
self.bound = va + La * (self.c - a)
boundcheck = vb + Lb * (self.c - b)
if abs(self.bound - boundcheck) > 0.01:
print("bound = ", self.bound, ", check ", boundcheck)
print("a = ", a, ", b = ", b, ", va = ", va, ", vb = ", vb,
", La = ", La, ", Lb = ", Lb)
print("s1 = ", s1)
print("s2 = ", s2)
def bnd(self):
return self.bound
def __repr__(self):
return "s1 = " + str(self.s1) + ", s2 = " + str(self.s2) + ", interval = " + str(self.ival)\
+ "c =" + str(self.c) + ", bound = " + str(self.bound)
f = smp.lambdify(problem.xvar, problem.fexpr)
fslp = smp.lambdify(problem.xvar, problem.fexpr, slp)
P = []
ival = interval.Interval(problem.range)
s1 = fslp(slp.Slope(ival, ival[0]))
s2 = fslp(slp.Slope(ival, ival[1]))
P.append(Sub(s1, s2, ival))
fr = solinfo.value
steps = 0
# Expr.flagRecompRange = True
while len(P) > 0 and steps <= maxsteps:
steps = steps + 1
sub = P.pop(0)
if fr - sub.bnd() > eps:
x1 = interval.Interval([sub.ival[0], sub.c])
x2 = interval.Interval([sub.c, sub.ival[1]])
# ns = fslp(slp.Slope(sub.ival, sub.c))
# ns1 = ns
# ns2 = ns
ns1 = fslp(slp.Slope(x1, sub.c))
ns2 = fslp(slp.Slope(x2, sub.c))
# print("at ", sub.c, " ns = ", ns)
if ns1.value < fr:
fr = ns1.value
xr = sub.c
P.append(Sub(sub.s1, ns1, x1))
P.append(Sub(ns2, sub.s2, x2))
solinfo.value = fr
solinfo.x = xr
return steps
def intervalize(par):
return [ival.Interval(e) for e in par]
def mkconst(val):
return ival.Interval([val, val])