def getHits(self, timestamp: int) -> int:
"""
Return the number of hits in the past 5 minutes.
@param timestamp - The current timestamp (in seconds granularity).
"""
i = bisect(self.t, [timestamp-300, float('inf')])-1
j = bisect(self.t, [timestamp,float('inf')])-1
return self.t[j][1] - self.t[i][1]
def blah(s, e):
print bisect_left(s, e)
print bisect_left(s, e, 0)
print bisect_left(s, e, 0, len(s))
print bisect_right(s, e)
print bisect(s, e)
insort_left(s, e)
insort_right(s, e)
insort(s, e)
print s
def blah(s, e):
print bisect_left(s, e)
print bisect_left(s, e, 0)
print bisect_left(s, e, 0, len(s))
print bisect_right(s, e)
print bisect(s, e)
insort_left(s, e)
insort_right(s, e)
insort(s, e)
print s
def getMachine(self,key):
h = self.hashfn(key)
i = bisect(self._hring, h)
if i >= len(self._hring): i = 0
m = self._hm[self._hring[i]]
#print 'key %s hash %s picking machine %s machine_hash %s index %s' % (key,h,m,self._hring[i],i)
return m
def findMin(end_dict=[], var=[1, 1, 1, 1]):
"""Main algorithm for solving problem
input 'end_dict': dictionary where keys are the unique packet end points
and value is a list of associated starting points
@input 'var': [n, size cost, constant cost, #of packets]
@output: min time to download data of size var[0] rounded to 3 decimals
also prints out this time (if it exists) rounded to 3 decimals
"""
times = {}
times[0] = float(0)
ends = end_dict.keys()
ends.sort()
for elem in ends:
times[elem] = float("inf")
right = bisect(ends, elem)
for ii in end_dict[elem]:
if(ii == 0): # for any n, the best solution will always be (0,n)
times[elem] = float(elem)/var[2] + 2*var[1]
else:
ii_const = float(elem - ii)/var[2]+2*var[1]
for j in range(bisect_left(ends, ii), bisect_left(ends, elem)):
j_const = ii_const + times[ends[j]]
if(j_const < times[elem]):
times[elem] = j_const
if((var[0] in times) and (times[var[0]] != float("inf"))):
print '{0:.3f}'.format(times[var[0]])
return(round(times[var[0]], 3))
else:
return(-1)
def p_e():
s = input()
t = input()
l = defaultdict(list)
for i, c in enumerate(list(s)):
l[c].append(i + 1)
for c in list(t):
if c not in l.keys():
print(-1)
exit()
N = 0
current = -1
for c in list(t):
R = l[c]
x = bisect(R, current)
if len(R) == x:
N += 1
current = R[0]
else:
current = R[x]
print(N * len(s) + current)
def closest_sorted(a, x, k): boundaryValue = sys.maxint #add boundary values into the list for right and left a.append(boundaryValue) a.insert(0, boundaryValue*-1) #insert the query element into the list #use build in binary search to get the index that it should be inserted into insertPosition=bisect(a, x) a.insert(insertPosition, x) result = [] left = insertPosition - 1 right = insertPosition + 1 while len(result) != k: if abs(a[right] - x) <= abs(a[left] - x): result.append(a[right]) right += 1 else: result.append(a[left]) left -= 1 return result
def __init__(self, waveReader, onsetSamples):
self.samples = waveReader.channels[0]
self.segments = []
self.onsets = [0]
crossings = [i for i in xrange(len(self.samples) - 1)
if self.samples[i] < 0 and self.samples[i+1] >= 0]
for onset in onsetSamples:
self.onsets.append(crossings[bisect(crossings, onset) - 1])
self.onsets = sorted(list(set(self.onsets)))
for i in xrange(len(self.onsets) - 1):
s = Segment(self.samples[self.onsets[i]:self.onsets[i+1]])
self.segments.append(s)
simMatrix = self.findNeighborMatrix()
smCopy = array(simMatrix, copy=True)
fill_diagonal(smCopy, 0)
sims = sorted(list(smCopy.reshape(-1)), reverse=True)[:TARGET_NUM_JUMPS]
SIMILARITY_THRESHOLD = sims[-1]
print 'Using similarity threshold = ', SIMILARITY_THRESHOLD
for i in xrange(len(self.segments)):
self.segments[i].neighbors = [j for j in xrange(len(simMatrix[i]))
if simMatrix[i][j] >= SIMILARITY_THRESHOLD and abs(i-j) > 10]
def prkdtree(points, xylim, center=None, depth=0):
if len(points)==1:
return PRKDTreeNode(xyrange=xylim,
center=center,
point=points[0],
left=None,
right=None)
if len(points)==0:
return PRKDTreeNode(xyrange=xylim,
center=center,
point=None,
left=None,
right=None)
k = len(points[0])
axis = depth % k
pmid = (xylim[axis][1]+xylim[axis][0])/2.0
points.sort(key=lambda points:points[axis])
P = [p[axis] for p in points]
pivot = bisect(P, pmid) # includes all <=
xmin,xmax=xylim[0][0], xylim[0][1]
ymin,ymax=xylim[1][0], xylim[1][1]
rangel = [ [xmin, xmax], [ymin, ymax] ]
rangel[axis][1] = pmid
ranger = [ [xmin, xmax], [ymin, ymax] ]
ranger[axis][0] = pmid
axis2 = (depth+1) % k
pmidl = (rangel[axis2][0]+rangel[axis2][1])/2.0
pmidr = (ranger[axis2][0]+ranger[axis2][1])/2.0
return PRKDTreeNode(xyrange = xylim,
center = pmid,
point = None,
left=prkdtree(points[:pivot],
rangel,pmidl,depth+1),
right=prkdtree(points[pivot:],
ranger,pmidr,depth+1))
def insertion_sort(A):
for j in range(1, len(A)):
key = A[j]
index = bisect(A,key,hi=j)
for i in range(j,index,-1):
A[i] = A[i-1]
A[index] = key
return A
def setValue(self, time, value):
i = bisect(self.times, time)
if i < len(self.times) and self.times[i] == time:
self.values[i] = value
else:
self.times.insert(i, time)
self.values.insert(i, value)
def find_next_joystick_release_time(trigger_time, mission):
start_idx = bisect(mission.joy_msgs.times, trigger_time)
for idx in range(start_idx, len(mission.joy_msgs) - 1):
if mission.joy_msgs.msgs[idx +
1].buttons[4] == 1 and mission.joy_msgs.msgs[
idx + 1].buttons[4] == 0:
return mission.joy_msgs.times[idx]
return mission.joy_msgs.times[-1]
def f():
r, z = input, int
M, N = r().split()
s = [z(r()) for x in '0' * z(M)]
m = max(s)
p = [y for y in [z(r()) for x in '0' * z(N)] if y < m]
l = sorted(y * p[x] for x in range(len(p)) for y in p[x:])
for i in s:
print(l[bisect(l, i - 1)] - i)
def bisect(targetWord):
fin = open('words.txt')
tempList = []
length = len(tempList)
for line in fin:
word = line.strip()
tempList.append(word)
#if the word is exactly in the middle, first try:
if targetWord == tempList[length/2]:
return tempList[length/2]
elif targetWord > tempList[length/2]:
bisect(targetWord)
elif targetWord < tempList[length/2]:
bisect(targetWord)
elif targetWord == tempList[i]:
return i
else:
return None
def solve():
primes = find_prime5(10 ** n)
primes = primes[bisect(primes, 10 ** (n - 1)):]
set_of_primes = set(primes)
pow_of_10 = [10 ** i for i in range(n)]
#mul_of_pow_of_10 = [[pow_of_10[i] * x for i in range(n)] for x in range(10)]
ls = [x for x in range(n - 1, -1, -1)]
def swap(n, combo, i):
pass
families = []
processed = set()
for p in primes:
ttsp = []
for i in range(n):
ttsp.append(p % 10 * pow_of_10[i])
p //= 10
ttsp.reverse()
cool = False
for combo in combinations(ls, k):
tsp = ttsp[:]
mask = 0
for x in combo:
mask += pow_of_10[n - x - 1]
tsp[x] = 0
masked = sum(tsp)
if (masked, mask) in processed:
continue
else:
processed.add((masked, mask))
family = []
for i in range(10):
pp = masked + mask * i
if pp in set_of_primes:
family.append(pp)
if len(family) == l:
families.append(family)
cool = True
break
if cool:
break
if families:
smallest = []
for family in families:
print(family)
if not smallest or family[0] < smallest[0]:
smallest = family
#if len(family) == l:
for prime in smallest:
#print(prime, end=' ')
print(prime)
def send_lines_at(time, channel, data):
"""send_line_at(time, channel, data) send out data at time on channel"""
g = DfGlobal()
buffer = g["data_channels_buffer"]
lines = [(time+g["viz_lag"],channel,dta) for dta in data.split("\n")]
position = bisect(buffer,(time+g["viz_lag"],channel,""))
new = buffer[:position]
new.extend(lines)
new.extend(buffer[position:])
g["data_channels_buffer"] = new
def insertion_sort(A):
for j in range(1, len(A)):
key = A[j]
k = bisect(A, key, 0, j)
for i in range(j, k - 1, -1):
A[i] = A[i - 1]
A[k] = key
#A = A[:k] + [key] + A[k:j] + A[j+1:]
return A
def solve(xs, field_length, num_ships, ship_length):
def num_accomodate(size):
return (size + 1) // (ship_length + 1)
bombed = [0, field_length+1]
holes = [field_length]
for i, x in enumerate(xs, 1):
pos = bisect(bombed, x)
holes = bomed[max(q - p - 1, 0) for (p, q) in zip(h, h[1:])]
def nth(n):
if n < 10:
return n
n -= 1
idx = bisect(base, n)
b = base[idx - 1]
remaining = n - b
position = remaining // (idx + 1)
num = 10 ** idx + position
return int(str(num)[remaining % (idx + 1)])
def nth(n):
if n < 10:
return n
n -= 1
idx = bisect(base, n)
b = base[idx - 1]
remaining = n - b
position = remaining // (idx + 1)
num = 10**idx + position
return int(str(num)[remaining % (idx + 1)])
def GetAccTime(tick, tempoList, tpb, prefixSum):
ret = 0
if (not hasattr(GetAccTime, "tickTable")):
GetAccTime.tickTable = []
for i in tempoList:
GetAccTime.tickTable.append(i[1])
index = bisect(GetAccTime.tickTable, tick)
ret = prefixSum[index - 1] + mido.tick2second(
tick - tempoList[index - 1][1], tpb, tempoList[index - 1][0])
return ret
def createrect(curdistincthlines):
curdistinctpaths = []
curdistincthlines = sorted(curdistincthlines)
length = len(curdistincthlines)
used = length * [0]
curdistincthlinesy = map(attrgetter('start.imag'), curdistincthlines)
for i in range(0, length):
if used[i] == 0:
intersectlines = []
intersectlines_ind = []
for k in range(i + 1, length):
if curdistincthlines[k].start.real == curdistincthlines[
i].start.real and curdistincthlines[
i].end.real == curdistincthlines[k].end.real:
intersectlines.append(curdistincthlines[k])
intersectlines_ind.append(k)
intersectlinesy = map(attrgetter('start.imag'), intersectlines)
nextstart = bisect(intersectlinesy, curdistincthlinesy[i])
lens = len(intersectlines)
if nextstart >= lens:
continue
nextend = bisect(intersectlinesy, intersectlinesy[nextstart])
if nextend > lens:
continue
for j in range(nextstart, nextend):
if used[intersectlines_ind[j]] == 0 and used[i] == 0:
if curdistincthlines[i].start.real == intersectlines[j].start.real and \
curdistincthlines[
i].end.real == \
intersectlines[j].end.real:
UperLine = curdistincthlines[i]
Lowerline = intersectlines[j]
newPath = Pattern(
UperLine, MicroLine(UperLine.end, Lowerline.end),
MicroLine(Lowerline.end, Lowerline.start),
MicroLine(Lowerline.start, UperLine.start))
used[intersectlines_ind[j]] = 1
used[i] = 1
curdistinctpaths.append(newPath)
return curdistinctpaths
def getValue(self, time):
if 0 == len(self.times):
return None
t = time % self.getPeriod()
i = bisect(self.times, t)
if i == len(self.times):
return lerp(self.times[i - 1], self.values[i - 1],
self.times[0] + self.getPeriod(), self.values[0], t)
return lerp(self.times[i - 1], self.values[i - 1],
self.times[i], self.values[i], t)
def xMasKranz(self):
dnitime = PtGetDniTime()
sdlName = xMasKranzsdl
sdl = PtGetAgeSDL()
sdl.setFlags(sdlName, 1, 1)
sdl.sendToClients(sdlName)
dayNum = int(time.strftime('%d', time.gmtime(dnitime)))
monthNum = int(time.strftime('%m', time.gmtime(dnitime)))
yearNum = int(time.strftime('%Y', time.gmtime(dnitime)))
dates = self.get_sunday_in_advent()
adventweek = bisect(dates, datetime.date(yearNum, monthNum, dayNum))
sdl.setIndex(sdlName, 0, adventweek)
PtDebugPrint(('codxMas: Current Adventweek is %d' % (adventweek)))
def get_testing_result(self, contours, color_img, bw_img):
width, height = bw_img.shape
#contours, hierarchy = cv2.findContours(bw_img,cv2.RETR_CCOMP,cv2.CHAIN_APPROX_SIMPLE)
#idx = 0 #just for writing to file needs
is_text_flags = []
# used for sorting
contour_left = []
filtered_contours = []
for cnt in contours:
area = cv2.contourArea(cnt)
if area > self.TEXT_AREA_THRESHOLD_LOWER and area < self.TEXT_AREA_THRESHOLD_UPPER:
x,y,w,h = cv2.boundingRect(cnt)
#sort contours by their left bound
i = bisect(contour_left, x)
contour_left.insert(i, x)
filtered_contours.insert(i, cnt)
feature1, feature2, feature3 = self.get_features(cnt, width, height)
crossings = self.get_horizontal_crossing(cnt, bw_img, color_img)
feature1 = np.array([feature1], np.float32)
feature2 = np.array([feature2], np.float32)
feature3 = np.array([feature3], np.float32)
feature4 = np.array(crossings, np.float32)
is_shape1 = self.svm1.predict(feature1)
is_shape2 = self.svm2.predict(feature2)
is_shape3 = self.svm3.predict(feature3)
is_shape4 = self.svm4.predict(feature4)
#is_text = not (is_shape1 and is_shape2 and is_shape3)
is_text = not (is_shape3 and is_shape4 and is_shape1 and is_shape2)
is_text_flags.append(is_text)
return filtered_contours, is_text_flags
from math import tan
from bisect import *
from rootsearch import *
f = lambda x: x - tan(x)
a, b, dx = (0, 20, 0.01)
print('The roots are:')
while True:
x1, x2 = rootsearch(f, a, b, dx)
if x1 != None:
a = x2
root = bisect(f, x1, x2, 1)
if root != None: print(root)
else:
print('\ndone!')
break
input('Press return to exit')
def FindPeakMutation(inputfile,outputfile,outputfileUTR3,tmp_ref_file,search_radius,promoter_radius,promoter_radius2,genome,adjacent,pwd,SNP,PromoterStop,NearestTwoDirection,UTR3):
print 'python process start:', datetime.now()
print 'Load Reference'
#######################################################
#update 05182015, reverse strand of reference gtf for UTR3
fout_reftmp = open(tmp_ref_file, 'w')
for line in open(pwd + 'gencode.' + genome + '.annotation_GENE_GTF.txt', 'r'):
line = line.strip().split('\t')
if line[6]=='+':
line[6] = '-'
elif line[6]=='-':
line[6] = '+'
else:
line[6] = '.'
for i in xrange(0,(len(line)-1)):
fout_reftmp.write(line[i] + '\t')
fout_reftmp.write(line[(len(line)-1)] + '\n')
fout_reftmp.close()
#######################################################
# Formatted output.
def out_string(peak, M, record, comment):
if record[6] == '+':
distance = a - M
else:
distance = b - M
return out_string_v2(peak, distance, record, comment)
def out_string_exon(peak, M, record, comment):
'''
if m<exona and n<exonb:
distance = n-exona
if m>=exona and n<exonb:
distance = n-m
if m>=exona and n>=exonb:
distance = exonb-m
if m<exona and n>=exonb:
distance = exonb-exona
'''
distance = [exona,exonb]
return out_string_v2(peak, distance, record, comment)
def out_string_intron(peak, M, record, comment):
'''
if m<introna and n<intronb:
distance = n-introna
if m>=introna and n<intronb:
distance = n-m
if m>=introna and n>=intronb:
distance = intronb-m
if m<introna and n>=intronb:
distance = intronb-introna
'''
distance = [introna,intronb]
return out_string_v2(peak, distance, record, comment)
def out_string_cds(peak, M, record, comment):
distance = [cdsa,cdsb]
return out_string_v2(peak, distance, record, comment)
def out_string_utr(peak, M, record, comment):
distance = [utra,utrb]
return out_string_v2(peak, distance, record, comment)
def out_string_v2(peak, distance, record, comment):
chromo, source, TSS, TTS, strand = record[0], record[1], record[3], record[4], record[6]
gene_name = record[8].strip().split(';')[1].strip().split(' ')[1][1:-1]
transcript_id = record[8].strip().split(';')[0].strip().split(' ')[1][1:-1]
gnote = reduce(lambda x, y: x + '\t' + y, [chromo, TSS, TTS, strand, gene_name, source, transcript_id])
return (peak + '\t' + str(n - m) + '\t' + str(distance) + '\t' + comment + '\t' + gnote)
######load exon, intron, geneid index information
geneid_set =[]
exonband =[]
intronband =[]
cdsband =[]
utrband =[]
for line in open(pwd + r'/GENCODE_' + genome + '_EXONinfo.txt','r'):
line = ast.literal_eval(line.strip().split('\t')[1])
exonband.append(line)
for line in open(pwd + r'/GENCODE_' + genome + '_INTRONinfo.txt','r'):
line = ast.literal_eval(line.strip().split('\t')[1])
intronband.append(line)
for line in open(pwd + r'/GENCODE_' + genome + '_CDSinfo.txt','r'):
line = ast.literal_eval(line.strip().split('\t')[1])
cdsband.append(line)
for line in open(pwd + r'/GENCODE_' + genome + '_UTRinfo.txt','r'):
line = ast.literal_eval(line.strip().split('\t')[1])
utrband.append(line)
for line in open(pwd + r'/GENCODE_' + genome + '_GENEID_index.txt','r'):
line = ast.literal_eval(line.strip().split('\t')[0])
geneid_set.append(line)
#index gemeid_set
genemap=dict()
geneset=set()
for i in xrange(len(geneid_set)):
key=geneid_set[i][1]
genemap[key] = geneid_set[i][0]
geneset.add(key)
print 'Check Reference files'
'''
PURPOSE
Read and parse transcript file.
PARAMETERS
TRANSCRIPT List of chromosomes; each chromosome itself is a list of transcript strand.
TRANSCRIPTLeft List of chromosomes; each chromosome itself is a list of lower index of transcript strand.
'''
TRANSCRIPT = []
TRANSCRIPTLeft = []
transcript_chrm = {}
ichrm = newChrmId = -1
##########update 05182015,UTR3 reference
if UTR3 == False:
reference_basedon_UTR = pwd + 'gencode.' + genome + '.annotation_GENE_GTF.txt'
elif UTR3 == True:
reference_basedon_UTR = tmp_ref_file
##########
for line in open(reference_basedon_UTR, 'r'):
line = line.strip().split('\t')
if line[0][3:] in transcript_chrm:
ichrm = transcript_chrm[ line[0][3:] ]
else:
newChrmId += 1
ichrm = newChrmId
transcript_chrm[ line[0][3:] ] = ichrm
TRANSCRIPT.append([])
TRANSCRIPTLeft.append([])
TRANSCRIPT[ichrm].append( line )
TRANSCRIPTLeft[ichrm].append( int(line[3]) )
'''
PURPOSE
Sort transcript by strand end id.
PARAMETERS
TRANSCRIPTRightSort List of chromosomes; each chromosome sorted by strand right location.
TRANSCRIPTRight List of chromosomes; each chromosome itself is a list of right location.
TRANSCRIPTRightId List of chromosomes; each chromosome itself is a list of exon id in the file.
'''
TRANSCRIPTRightSort = []
TRANSCRIPTRight = []
TRANSCRIPTRightID = []
for transcript in TRANSCRIPT:
TRANSCRIPTRightSort.append([])
TRANSCRIPTRight.append([])
TRANSCRIPTRightID.append([])
for i in xrange(len(transcript)):
TRANSCRIPTRightSort[-1].append( (int(transcript[i][4]), i) )
TRANSCRIPTRightSort[-1].sort(key = lambda x: x[0])
for key in TRANSCRIPTRightSort[-1]:
TRANSCRIPTRight[-1].append(key[0])
TRANSCRIPTRightID[-1].append(key[1])
'''
PURPOSE
Prepare lists of begin id & key for all genes and for protein genes.
PARAMETERS
TSBEGIN List of chromosome; each chromosome itself a list of (arrow begin index, line number in the transcript).
TSBEGINKEY List of chromosome; each chromosome itself a list of (arrow begin index).
TSLINEID List of chromosome; each chromosome itself a list of (line number in the transcript).
PCBEGIN, PCBEGINKEY, PCLINEID Same as above, but for protein codings.
'''
TSBEGIN = []
TSBEGINKEY = []
TSLINEID = []
PCBEGIN = []
PCBEGINKEY = []
PCLINEID = []
for transcript in TRANSCRIPT:
TSBEGIN.append([])
TSBEGINKEY.append([])
TSLINEID.append([])
PCBEGIN.append([])
PCBEGINKEY.append([])
PCLINEID.append([])
for i in xrange(len(transcript)):
record = transcript[i]
# Append to gene list.
if record[6] == '+':
begin = int(record[3])
else:
begin = int(record[4])
TSBEGIN[-1].append( (begin, i) )
# Append to protein coding gene list.
if record[1] == 'protein_coding':
PCBEGIN[-1].append( (begin, i) )
TSBEGIN[-1].sort(key = lambda x: x[0])
for key in TSBEGIN[-1]:
TSBEGINKEY[-1].append(key[0])
TSLINEID[-1].append(key[1])
PCBEGIN[-1].sort(key = lambda x: x[0])
for key in PCBEGIN[-1]:
PCBEGINKEY[-1].append(key[0])
PCLINEID[-1].append(key[1])
'''
PURPOSE
Parse the peak file.
ALGORITHM
(1) Identify exon;
(2) Identify intron; CDS;UTR
(3) Find nearest protein coding;
(4) Find neighbors within a range.
'''
print 'fixed reference done:', datetime.now()
fout = open(outputfile,'w')
print 'Start Annotation'
count = -1
for line in open(inputfile, 'r'):
# Neglect the comment line.
count += 1
if count == 0:
sline =line.strip().split('\t')
fout.write(sline[0] + '\t' +sline[1] + '\t' +sline[2] + '\t' +sline[3] + '\t' )
fout.write('PeakLength' + '\t' + 'peakMtoStart_Overlap' + '\t' + 'type' + '\t' + 'BidirenctionalRegion' + '\t')
fout.write('Chr' + '\t' + 'TSS' + '\t' + 'TTS' + '\t' + 'strand' + '\t' + 'gene_name' + '\t' + 'source'+ '\t' + 'transID' + '\n')
continue
# ---------------------------------------
# Parse the peak information (m < n).
#
# middle
# |
# ---m---------n---
#
# ---------------------------------------
line = line.strip().split()
pkchrm = line[1]
if pkchrm[0:3].upper() == 'CHR':
pkchrm = pkchrm[3:]
m, n = int(line[2]), int(line[3])
middle = (m + n) / 2
peakLeft = m
peakRight = n
# The information about the peak to be printed.
pkhd = reduce(lambda x, y: x + '\t' + y, line[0:4])
# ---------------------------------------
# Annotate exon;intron
# ---------------------------------------
# Check if the chromosome has been registered.
if pkchrm not in transcript_chrm:
print pkchrm, 'Chromosome not registered'
continue
else:
ichrm = transcript_chrm[ pkchrm ]
transcript = TRANSCRIPT[ichrm]
transcriptLeft = TRANSCRIPTLeft[ichrm]
transcriptRight = TRANSCRIPTRight[ichrm]
transcriptRightID = TRANSCRIPTRightID[ichrm]
# A set holding everything that has been marked.
myNeighbor = set()
# Find the search range.
iMin = bisect_left(transcriptRight, peakLeft)
setRight = set()
for i in xrange(iMin, len(transcriptRight)):
setRight.add(transcriptRightID[i])
iMax = bisect_right(transcriptLeft, peakRight, lo=iMin+1)
setLeft = set(range(iMax))
# Search the range.
found_exon_protein = False
found_intron_protein = False
#search exon region
for transcriptID in setRight.intersection(setLeft):
record = transcript[transcriptID]
a, b = int(record[3]), int(record[4])
if n < a or m > b:
continue
else:
geneid_B=transcript[transcriptID][8].strip().split(';')[0][9:-1]
if len(exonband[genemap[geneid_B]])>0:
for i in xrange(len(exonband[genemap[geneid_B]])):
exona=exonband[genemap[geneid_B]][i][0]
exonb=exonband[genemap[geneid_B]][i][1]
if n < exona or m > exonb:
pass
else:
fout.write(out_string_exon(pkhd, middle, record, 'Exon\tNA')+ '\n')
#Check when exon finds, make stop label for SNP and adjacent=True
if record[1] == 'protein_coding':
if adjacent == True or SNP == True:
found_exon_protein = True
myNeighbor.add(transcriptID)
#search intron region
if found_exon_protein == False:
for transcriptID in setRight.intersection(setLeft):
record = transcript[transcriptID]
a, b = int(record[3]), int(record[4])
if n < a or m > b:
continue
else:
geneid_B=transcript[transcriptID][8].strip().split(';')[0][9:-1]
if len(intronband[genemap[geneid_B]])>0:
for i in xrange(len(intronband[genemap[geneid_B]])):
introna=intronband[genemap[geneid_B]][i][0]
intronb=intronband[genemap[geneid_B]][i][1]
if n < introna or m > intronb:
pass
else:
fout.write(out_string_intron(pkhd, middle, record, 'Intron\tNA')+ '\n')
#Check when intron finds, make stop label for adjacent=True
if record[1] == 'protein_coding':
if adjacent == True:
found_intron_protein = True
myNeighbor.add(transcriptID)
#search cds region
if found_exon_protein == False and found_intron_protein == False:
for transcriptID in setRight.intersection(setLeft):
record = transcript[transcriptID]
a, b = int(record[3]), int(record[4])
if n < a or m > b:
continue
else:
geneid_B=transcript[transcriptID][8].strip().split(';')[0][9:-1]
if len(cdsband[genemap[geneid_B]])>0:
for i in xrange(len(cdsband[genemap[geneid_B]])):
cdsa=cdsband[genemap[geneid_B]][i][0]
cdsb=cdsband[genemap[geneid_B]][i][1]
if n < cdsa or m > cdsb:
pass
else:
fout.write(out_string_cds(pkhd, middle, record, 'cds\tNA')+ '\n')
myNeighbor.add(transcriptID)
#search utr region
if found_exon_protein == False and found_intron_protein == False:
for transcriptID in setRight.intersection(setLeft):
record = transcript[transcriptID]
a, b = int(record[3]), int(record[4])
if n < a or m > b:
continue
else:
geneid_B=transcript[transcriptID][8].strip().split(';')[0][9:-1]
if len(utrband[genemap[geneid_B]])>0:
for i in xrange(len(utrband[genemap[geneid_B]])):
utra=utrband[genemap[geneid_B]][i][0]
utrb=utrband[genemap[geneid_B]][i][1]
if n < utra or m > utrb:
pass
else:
fout.write(out_string_utr(pkhd, middle, record, 'utr\tNA')+ '\n')
myNeighbor.add(transcriptID)
#############################
#search internal-promoter region
if found_exon_protein == False and found_intron_protein == False:
for transcriptID in setRight.intersection(setLeft):
record = transcript[transcriptID]
a, b = int(record[3]), int(record[4])
if n < a or m > b:
continue
else:
if record[6] == '+':
if m < a + promoter_radius2:
fout.write(out_string(pkhd, middle, record, 'Promoter_internal\tNA')+ '\n')
myNeighbor.add(transcriptID)
elif record[6] == '-':
if n > b - promoter_radius2:
fout.write(out_string(pkhd, middle, record, 'Promoter_internal\tNA')+ '\n')
myNeighbor.add(transcriptID)
#####################################
# If found protein_coding. Annotate the next peak.
if found_exon_protein or found_intron_protein:
continue
# --------------------------------------------
# Search promoter in protein coding genes.
# --------------------------------------------
pcbeginkey = PCBEGINKEY[ichrm]
pclineid = PCLINEID[ichrm]
pcid = bisect(pcbeginkey, middle)
# Find the left promoter.
i = pcid - 1
found_left_promoter, left_d = False, 0
left_promoter = []
while i >= 0 and not found_left_promoter and left_d < promoter_radius:
record = transcript[ pclineid[i] ]
a, b = int(record[3]), int(record[4])
left_d = m - b
if left_d < promoter_radius:
if record[6] == '-':
found_left_promoter = True
left_promoter.append( record )
i = i - 1
# Print the non-nearest left promoters.
for record in left_promoter[1:]:
a, b = int(record[3]), int(record[4])
#print out_string(pkhd, middle, record, 'Promotor_L\tN')
fout.write(out_string(pkhd, middle, record, 'Promoter_L\tN')+ '\n')
# Find the right promoter.
i = pcid
found_right_promoter, right_d = False, 0
right_promoter = []
while i < len(pcbeginkey) and not found_right_promoter and right_d < promoter_radius:
record = transcript[ pclineid[i] ]
a, b = int(record[3]), int(record[4])
right_d = a - n
if right_d < promoter_radius:
if record[6] == '+':
found_right_promoter = True
right_promoter.append( record )
i = i + 1
# Print the non-nearest right promoters.
for record in right_promoter[1:]:
a, b = int(record[3]), int(record[4])
#print out_string(pkhd, middle, record, 'Promotor_R\tN')
fout.write(out_string(pkhd, middle, record, 'Promoter_R\tN') + '\n')
# If promoters are found on both sides.
if found_left_promoter and found_right_promoter:
record = left_promoter[0]
a, b = int(record[3]), int(record[4])
#print out_string(pkhd, middle, record, 'Promotor_L\tY')
fout.write(out_string(pkhd, middle, record, 'Promoter_L\tY') + '\n')
record = right_promoter[0]
a, b = int(record[3]), int(record[4])
#print out_string(pkhd, middle, record, 'Promotor_R\tY')
fout.write(out_string(pkhd, middle, record, 'Promoter_R\tY')+ '\n')
# Find the right nearest neighbor if no right promoter found.
if found_left_promoter and not found_right_promoter:
is_right_bidirectional = False
i = pcid
found_right = False
while i < len(pcbeginkey) and not found_right:
record = transcript[ pclineid[i] ]
a, b = int(record[3]), int(record[4])
if min(a, b) > n:
found_right = True
if record[6] == '+':
is_right_bidirectional = True
#print out_string(pkhd, middle, record, 'Nearest_R\tY')
fout.write(out_string(pkhd, middle, record, 'Nearest_R\tY') + '\n')
else:
#print out_string(pkhd, middle, record, 'Nearest_R\tN')
fout.write(out_string(pkhd, middle, record, 'Nearest_R\tN') + '\n')
else:
i = i + 1
record = left_promoter[0]
a, b = int(record[3]), int(record[4])
if is_right_bidirectional:
#print out_string(pkhd, middle, record, 'Promotor_L\tY')
fout.write(out_string(pkhd, middle, record, 'Promoter_L\tY') + '\n')
else:
#print out_string(pkhd, middle, record, 'Promotor_L\tN')
fout.write(out_string(pkhd, middle, record, 'Promoter_L\tN') + '\n')
# Find the left nearest neighbor if no left promoter found.
if not found_left_promoter and found_right_promoter:
is_left_bidirectional = False
i = pcid - 1
found_left = False
while i >= 0 and not found_left:
record = transcript[ pclineid[i] ]
a, b = int(record[3]), int(record[4])
if max(a, b) < m:
found_left = True
if record[6] == '-':
is_left_bidirectional = True
#print out_string(pkhd, middle, record, 'Nearest_L\tY')
fout.write(out_string(pkhd, middle, record, 'Nearest_L\tY') + '\n')
else:
#print out_string(pkhd, middle, record, 'Nearest_L\tN')
fout.write(out_string(pkhd, middle, record, 'Nearest_L\tN') + '\n')
else:
i = i - 1
record = right_promoter[0]
a, b = int(record[3]), int(record[4])
if is_left_bidirectional:
#print out_string(pkhd, middle, record, 'Promotor_R\tY')
fout.write(out_string(pkhd, middle, record, 'Promoter_R\tY') + '\n')
else:
#print out_string(pkhd, middle, record, 'Promotor_R\tN')
fout.write(out_string(pkhd, middle, record, 'Promoter_R\tN') + '\n')
# Stop here if any promoter is found and if PromoterStop index is True, else if no promoter is found/or PromoterStop index is False, contitue for further
# search in search radius.
if PromoterStop == False:
found_left_promoter = PromoterStop
found_right_promoter = PromoterStop
elif PromoterStop == True:
pass
if found_left_promoter or found_right_promoter:
continue
# ----------------------------------------------------
# Search nearest neighbor in protein coding genes.
# ----------------------------------------------------
# Find the left nearest transcript.
i = pcid - 1
found_left = False
while i >= 0 and not found_left:
lineL = pclineid[i]
record = transcript[lineL]
a, b = int(record[3]), int(record[4])
if max(a, b) < m:
found_left = True
else:
i = i - 1
# Find the right nearest transcript.
i = pcid
found_right = False
while i < len(pcbeginkey) and not found_right:
lineR = pclineid[i]
record = transcript[lineR]
a, b = int(record[3]), int(record[4])
if min(a, b) > n:
found_right = True
else:
i = i + 1
# Check if is bidirectional.
if found_left and found_right:
recordL = transcript[lineL]
recordR = transcript[lineR]
if recordL[6] == '-' and recordR[6] == '+':
a, b = int(recordL[3]), int(recordL[4])
myNeighbor.add(lineL)
#print out_string(pkhd, middle, recordL, 'Nearest_L\tY')
fout.write(out_string(pkhd, middle, recordL, 'Nearest_L\tY') + '\n')
a, b = int(recordR[3]), int(recordR[4])
myNeighbor.add(lineR)
#print out_string(pkhd, middle, recordR, 'Nearest_R\tY')
fout.write(out_string(pkhd, middle, recordR, 'Nearest_R\tY') + '\n')
else:
a, b = int(recordL[3]), int(recordL[4])
if recordL[6] == '+':
dL = a - middle
else:
dL = b - middle
a, b = int(recordR[3]), int(recordR[4])
if recordR[6] == '+':
dR = a - middle
else:
dR = b - middle
if NearestTwoDirection == False:
if abs(dL) < abs(dR):
#print out_string_v2(pkhd, dL, recordL, 'Nearest_L\tN')
fout.write(out_string_v2(pkhd, dL, recordL, 'Nearest\tN') + '\n')
myNeighbor.add(lineL)
else:
#print out_string_v2(pkhd, dR, recordR, 'Nearest_R\tN')
fout.write(out_string_v2(pkhd, dR, recordR, 'Nearest\tN') + '\n')
myNeighbor.add(lineR)
if NearestTwoDirection == True:
fout.write(out_string_v2(pkhd, dL, recordL, 'Nearest_L\tN') + '\n')
fout.write(out_string_v2(pkhd, dR, recordR, 'Nearest_R\tN') + '\n')
myNeighbor.add(lineL)
myNeighbor.add(lineR)
elif found_left:
myNeighbor.add(lineL)
record = transcript[lineL]
a, b = int(record[3]), int(record[4])
myNeighbor.add(lineL)
#print out_string(pkhd, middle, record, 'Nearest_L\tN')
fout.write(out_string(pkhd, middle, record, 'Nearest\tN') + '\n')
elif found_right:
myNeighbor.add(lineR)
record = transcript[lineR]
a, b = int(record[3]), int(record[4])
myNeighbor.add(lineR)
#print out_string(pkhd, middle, record, 'Nearest_R\tN')
fout.write(out_string(pkhd, middle, record, 'Nearest\tN')+ '\n')
# -------------------------------------------
# Print everything within searching radius.
# -------------------------------------------
tsbeginkey = TSBEGINKEY[ichrm]
tslineid = TSLINEID[ichrm]
lower_bound = max(0, middle - search_radius)
upper_bound = min(tsbeginkey[-1], middle + search_radius)
lower_id = bisect(tsbeginkey, lower_bound)
upper_id = bisect(tsbeginkey, upper_bound, lo = lower_id)
for key_id in xrange(lower_id, upper_id):
line_id = tslineid[key_id]
if line_id not in myNeighbor:
distance = middle - tsbeginkey[key_id]
record = transcript[line_id]
#print out_string_v2(pkhd, distance, record, 'Neighbor\tN')
fout.write(out_string_v2(pkhd, distance, record, 'Neighbor\tN') + '\n')
fout.close()
####update 05182015 UTR3
fout_utr = open(outputfileUTR3,'w')
if UTR3 == False:
for line in open(outputfile,'r'):
fout_utr.write(line)
elif UTR3 == True:
nline =0
for line in open(outputfile,'r'):
nline +=1
if nline ==1:
fout_utr.write(line)
else:
line = line.strip().split('\t')
if line[11]=='+':
line[11] = '-'
elif line[11]=='-':
line[11] = '+'
else:
line[11] = '.'
for i in xrange(0,(len(line)-1)):
fout_utr.write(line[i] + '\t')
fout_utr.write(line[(len(line)-1)] + '\n')
fout_utr.close()
####
print 'Finish Annotation'
print 'python process end:', datetime.now()
print >> sys.stderr, "failed extracting acc info for %s" % r.id
for file in os.listdir(igr_dirname):
#acc = file[:file.find('.')]
for r in SeqIO.parse(open(igr_dirname+'/'+file),'fasta'):
m = rex.match(r.id)
acc = m.group(1)
i = acc.find('.')
if i > 0: acc = acc[:i]
ok_random = False
if acc in ribo_acc_set:
if no_ambiguous_code(r.seq.tostring()):
start = int(m.group(2))
end = int(m.group(3))
if min_len <= end-start <= max_len:
i = bisect(ribo_acc_set[acc],(start,end))
if i == 0:
ok_random = end < ribo_acc_set[acc][0][0]
elif i == len(ribo_acc_set[acc])-1:
ok_random = ribo_acc_set[acc][-1][1] < start
elif i <= len(ribo_acc_set[acc])-2:
ok_random = ribo_acc_set[acc][i-1][1] < start and end < ribo_acc_set[acc][i][0]
else:
ok_random = ribo_acc_set[acc][i-1][1] < start
else:
ok_random = True
if ok_random:
print ">%s\n%s" % (r.id,r.seq.tostring())
from bisect import *
p = [1]*300003
p[0] = p[1] = 0
for i in xrange(2,300003):
if p[i] and i%7 in (1,6):
p[2*i::i] = [0]*len(p[2*i::i])
else:
p[i] = 0
p = [i for i in xrange(2,300003) if p[i]]
while 1:
N = int(raw_input())
if N == 1: break
ans = [i for i in p[:bisect(p,N+1)] if N%i == 0]
print "%d: %s"%(N," ".join(map(str,ans)))
#coding=utf-8 import bisect ''' 利用二分法维持sorted的list bisect(list, item[, lo[, hi]]) list为sorted的, lo和hi为list的边界, 默认为整个list ''' aray = [1, 2, 3, 4, 5] index = bisect.bisect_left(aray, 3) #遇到相等的item返回左边的index index = bisect.bisect_right(aray, 3) #遇到相等的item返回右边的index #通过bisect得到index后，调用list.insert()实现 bisect.insort_left(aray, 2.5) #遇到相等的item插入左边的index bisect.insort_right(aray, 3) #遇到相等的item插入右边的index
def add(self, value):
i = bisect(self, value)
if i==0 or self[i-1] <> value: self.insert(i, value)
#!/usr/bin/env python
def bisect(alist, word):
left = 0
right = len(alist) - 1
while left < right:
now = (left + right) / 2
#print left, ' ', right, ' ', now, ' ', alist[now], ' ', word
if alist[now] == word:
return now
elif alist[now] > word:
right = now - 1
else:
left = now + 1
return None
word_list = []
dict_file = open('../data/words.txt')
for e in dict_file:
word_list.append(e.strip())
print bisect(word_list, 'boy')
import bisect
print bisect.bisect(word_list, 'boy') - 1
from bisect import * n = [1, 2, 3, 4, 5] print bisect(n, 1) print bisect(n, 5)
from bisect import *
R = 200001
p = [1]*R
p[0] = p[1] = 0
for i in xrange(2,int(R**0.5)):
if p[i]: p[2*i::i] = [0]*(len(p[2*i::i]))
p = [i for i in xrange(2,R) if p[i]]
K = int(raw_input())
N = int(raw_input())
ans = mx = 0
H = []
for i in xrange(bisect(p,K),bisect(p,N)):
s = str(p[i])
while len(s) > 1:
s = str(sum(map(int,list(s))))
if s in H:
if len(H) > mx: mx,ans = len(H),p[i-len(H)]
elif len(H) == mx: ans = max(ans, p[i-len(H)])
while s in H:
H.pop(0)
H.append(s)
else:
if len(H) > mx: ans = p[i+1-len(H)]
elif len(H) == mx: ans = max(ans, p[i+1-len(H)])
print ans
def grade(score, breakpoints=[60,70,80,90], grades="FDCBA"): i=bisect(breakpoints, score) return grades[i]
def getValue(self, time):
i = bisect(self.times, time % self.getPeriod())
return self.values[i - 1]
def triplets(a, b, c):
a, c = sorted(set(a)), sorted(set(c))
return sum([bisect(a, x) * bisect(c, x) for x in set(b)])
def generate(self):
for i in range(0, len(self.list3)):
pos = bisect(self.list4, self.list3[i])
for e in range(pos, len(self.list4)):
yield self.list1[i] + self.list2[e]
return primes from bisect import * times = input() params = [] m = 0 for i in range(times): a = input() m = max(m, a) params.append(a) ar = get_primes(m) ar.sort() ar2 = [] accu = 0 for i in ar: accu += i ar2.append(accu) for item in params: n = item index = bisect(ar, n) if index <= 0: print 0 else: print ar2[index - 1]