def get_fn(self, arity):
f = self._arities.get(arity, None)
if f is not None:
return f
if self._rest_fn is not None and arity >= self._required_arity:
return self._rest_fn
acc = []
sorted = TimSort(self.get_arities())
sorted.sort()
for x in sorted.list:
acc.append(unicode(str(x)))
if self._rest_fn:
acc.append(unicode(str(self._rest_fn.required_arity())) + u"+")
runtime_error(u"Wrong number of arguments " + unicode(str(arity)) + u" for function '" + unicode(self._name) + u"'. Expected " + join_last(acc, u"or"))
def get_fn(self, arity):
f = self._arities.get(arity, None)
if f is not None:
return f
if self._rest_fn is not None and arity >= self._required_arity:
return self._rest_fn
acc = []
sorted = TimSort(self.get_arities())
sorted.sort()
for x in sorted.list:
acc.append(unicode(str(x)))
if self._rest_fn:
acc.append(unicode(str(self._rest_fn.required_arity())) + u"+")
runtime_error(u"Wrong number of arguments " + unicode(str(arity)) + u" for function '" + unicode(self._name) + u"'. Expected " + join_last(acc, u"or"),
u"pixie.stdlib/InvalidArityException")
def sorttest(lst1):
lst2 = lst1[:]
TimSort(lst2).sort()
assert len(lst1) == len(lst2)
assert makeset(lst1) == makeset(lst2)
position = {}
i = 0
for a in lst1:
position.setdefault(id(a), []).append(i)
i += 1
for i in range(len(lst2) - 1):
a, b = lst2[i], lst2[i + 1]
assert a <= b, "resulting list is not sorted"
if a == b:
assert position[id(a)][0] < position[id(b)][-1], "not stable"
def __init__(self, space, list, listlength=None, sortblock=None):
TimSort.__init__(self, list, listlength=listlength)
self.space = space
self.sortblock = sortblock
def __init__(self, list, listlength=None, compare_fn=None, ctx=None):
TimSort.__init__(self, list, listlength)
self.compare_fn = compare_fn
self.ctx = ctx
def fq2c(qry):
ksize = max(2, int(qry[0]))
names = qry[1:]
D = len(names)
scale = 4
#buck = [array('H', [0]) * pow(scale, k) for elem in xrange(D // 2)]
#buck = [array('H', [0]) * scale ** k for elem in xrange(D // 2)]
#buck = np.zeros((D//2, scale ** k), 'int32')
N = int(pow(scale, ksize))
buck = [[r_ushort(0) for elem0 in xrange(N)] for elem1 in xrange(D // 2)]
print 'ksize, names, D, N, buck shape', ksize, names, D, N, len(buck), len(buck[0])
flag = 0
itr = 1
init0 = init1 = time()
# for name0, name1 in zip(names[0::2], names[1::2]):
for i in xrange(0, len(names), 2):
name0, name1 = names[i], names[i + 1]
print 'qry0', name0, 'qry1', name1
f0 = open(name0, 'r')
f1 = open(name1, 'r')
seqs0 = parse(f0, 'fastq')
#seqs0 = SeqIO.parse(f0, 'fastq')
seqs1 = parse(f1, 'fastq')
#seqs1 = SeqIO.parse(f1, 'fastq')
for seq0, seq1 in izip([seqs0, seqs1]):
if seq0.qual.count('N') > 20 or seq1.qual.count('N') > 20:
continue
kmc(seq0.seq, buck[flag], ksize, scale)
kmc(seq1.seq, buck[flag], ksize, scale)
# timing
if itr % 1000000 == 0:
print 'iteration', itr, 'time', time() - init1, 'total time', time() - init0
init1 = time()
itr += 1
f0.close()
f1.close()
flag += 1
# print 'buck', [[intmask(b1) for b1 in b0] for b0 in buck]
# convert the each reads to a freq hist
flag = 0
itr = 1
init0 = init1 = time()
# for name0, name1 in zip(names[0::2], names[1::2]):
for i in xrange(0, len(names), 2):
name0, name1 = names[i], names[i + 1]
print 'qry0', name0, 'qry1', name1
f0 = open(name0, 'r')
f1 = open(name1, 'r')
seqs0 = parse(f0, 'fastq')
#seqs0 = SeqIO.parse(f0, 'fastq')
seqs1 = parse(f1, 'fastq')
#seqs1 = SeqIO.parse(f1, 'fastq')
for seq0, seq1 in izip([seqs0, seqs1]):
if seq0.qual.count('N') > 20 or seq1.qual.count('N') > 20:
continue
output = []
fwd = [intmask(buck[flag][elem])
for elem in seq2n(seq0.seq, ksize, scale, code)]
rev = [intmask(buck[flag][elem])
for elem in seq2n(seq1.seq, ksize, scale, code)]
med = len(fwd) // 2
step = 16
start, end = max(0, med - step), max(0, med + step)
# for test, only keep positive
output = fwd[start: end] + rev[start: end]
#output = fwd[start: end]
# output.sort()
TimSort(output).sort()
if len(output) < step * 2:
output.extend([0] * (step * 2 - len(output)))
# print max(output), min(output), mean(output), std(output), output
#A, B, C, D = khist(output)
# print ' '.join(map(str, A + ['|', B, C, D]))
# print ' '.join(map(str, output))
print 'output', ' '.join([str(out) for out in output])
# timing
if itr % 1000000 == 0:
print 'iteration', itr, 'time', time() - init1, 'total time', time() - init0
init1 = time()
itr += 1
f0.close()
f1.close()
flag += 1
return buck
def run(n, qry):
ksize = max(2, n)
rg = rrandom.Random()
a = []
for i in xrange(n):
#b = [r_ushort(int(rg.random() * pow(2, 15) - 1)) for elem0 in xrange(32)]
b = [int(rg.random() * pow(2, 15) - 1) for elem0 in xrange(32)]
# b.sort()
TimSort(b).sort()
# a.append(b)
a.append([r_ushort(elem) for elem in b])
# a.append(d)
#a = [TimSort([r_ushort(int(rg.random() * pow(2, 15) - 1)) for elem0 in xrange(32)]).sort() for elem1 in xrange(n)]
# print 'short add', a[0][0] + a[0][0]
u = p = 0
Atmp = range(6)
dna = 'atgcgc'
qsort(Atmp, dna)
print 'qsort', Atmp, [dna[elem] for elem in Atmp]
for i in xrange(1):
x = [0] * 32
y = [0] * 32
# for j in xrange(32):
# x[j] = rg.random()
# y[j] = rg.random()
#x = [rg.random() for elem in xrange(32)]
#y = [rg.random() for elem in xrange(32)]
#x = [intmask(elem) for elem in [r_ushort(0)] * 32]
#x = map(intmask, [0] * 32)
y = [intmask(elem) for elem in xrange(32)]
#rgs = range(32)
#y = map(intmask, rgs)
#x = y = [0] * 32
u, p = mannwhitneyu(x, y, True)
p = pearson(x, y)
print 'p value is', u, p
print k2n('ta' * 12), intmask(int('123'))
test_seq = 'tgatcgctgtagctgatgctcatgctatgctatcgtagtcgtgctagctagcatcgatcgatcgctagaaacagctgcgtatctatctatatatatattaggagaatgtgagaga'
test_n = seq2n(test_seq)
# for i in test_n:
# print 'seq2n test', i
canopy(a)
print [r_uint(elem) for elem in test_n]
buck = [[r_ushort(0) for elem0 in xrange(pow(scale, ksize))]
for elem1 in xrange(len(qry))]
f0 = open(qry, 'r')
f1 = open(qry, 'r')
seqs0 = parse(f0)
seqs1 = parse(f1)
for seq0, seq1 in izip([seqs0, seqs1]):
# print seq0.seq, seq1.seq
print 'test seq2n'
# print [nb for nb in seq2n(seq0.seq)]
kmc(seq0.seq, buck[0], ksize, scale)
kmc(seq1.seq, buck[0], ksize, scale)
f0.close()
f1.close()
print [intmask(elem) for elem in buck[0][:15]]
'''
def listsort():
lst = [10, 1, 9, 2, 8, 3, 7, 4, 5, 6]
TimSort(lst).sort()
print lst