def __init__(self,
particleEffect,
parent,
worldRelative=1,
renderParent=None,
duration=0.0,
softStopT=0.0,
cleanup=False,
name=None):
"""
particleEffect is a ParticleEffect
parent is a NodePath: this is where the effect will be
parented in the scenegraph
worldRelative is a boolean: this will override 'renderParent'
with render
renderParent is a NodePath: this is where the particles will
be rendered in the scenegraph
duration is a float: for the time
softStopT is a float: no effect if 0.0,
a positive value will count from the
start of the interval,
a negative value will count from the
end of the interval
cleanup is a boolean: if True the effect will be destroyed
and removed from the scenegraph upon
interval completion
set to False if planning on reusing
the interval
name is a string: use this for unique intervals so that
they can be easily found in the taskMgr
"""
# Generate unique name
id = 'Particle-%d' % ParticleInterval.particleNum
ParticleInterval.particleNum += 1
if name == None:
name = id
# Record instance variables
self.particleEffect = particleEffect
self.cleanup = cleanup
if parent != None:
self.particleEffect.reparentTo(parent)
if worldRelative:
renderParent = render
if renderParent:
for particles in self.particleEffect.getParticlesList():
particles.setRenderParent(renderParent.node())
self.__softStopped = False
if softStopT == 0.0:
self.softStopT = duration
elif softStopT < 0.0:
self.softStopT = duration + softStopT
else:
self.softStopT = softStopT
# Initialize superclass
Interval.__init__(self, name, duration)
def __init__(self,
particleEffect,
duration=0.0,
parent=None,
renderParent=None,
name=None):
"""
particleEffect is ??
parent is ??
worldRelative is a boolean
loop is a boolean
duration is a float for the time
name is ??
"""
# Generate unique name
id = 'Particle-%d' % TestInterval.particleNum
TestInterval.particleNum += 1
if name == None:
name = id
# Record instance variables
self.particleEffect = particleEffect
self.parent = parent
self.renderParent = renderParent
Interval.__init__(self, name, duration)
def privInitialize(self, t):
self.__initialize()
if self.collNode:
self.collNode.clearSolids()
csolid = CollisionParabola(self.parabola, 0, 0)
self.collNode.addSolid(csolid)
Interval.privInitialize(self, t)
def __init__(self,
node,
startPos=None,
endPos=None,
duration=None,
startVel=None,
endZ=None,
wayPoint=None,
timeToWayPoint=None,
gravityMult=None,
name=None,
collNode=None):
self.node = node
self.collNode = collNode
if self.collNode:
if isinstance(self.collNode, NodePath):
self.collNode = self.collNode.node()
if name == None:
name = '%s-%s' % (self.__class__.__name__,
self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
args = (startPos, endPos, duration, startVel, endZ, wayPoint,
timeToWayPoint, gravityMult)
self.implicitStartPos = 0
if startPos is None:
if duration is None:
self.notify.error('must provide either startPos or duration')
self.duration = duration
self.trajectoryArgs = args
self.implicitStartPos = 1
else:
self.trajectoryArgs = args
self.__calcTrajectory(*args)
Interval.__init__(self, name, self.duration)
return
def trim_back_edges(self, u: str):
"""
Remove back edges ending at parent u (phase 2)
@param u:
@return:
"""
# drop entire conflict pairs
while len(self.s) and self.lowest(self.top_s()) == self.height[u]:
p = self.s.pop()
if p.l.low is not None:
self.side[p.l.low] = -1
# one more conflict pair to consider
if len(self.s):
p = self.s.pop()
# trim left interval
while p.l.high is not None and p.l.high[1] == u:
p.l.high = self.ref[p.l.high]
if p.l.high is None and p.l.low is not None: # just emptied
self.ref[p.l.low] = p.r.low
self.side[p.l.low] = -1
p.l = Interval(high=p.l.high)
# trim right interval
while p.r.high is not None and p.r.high[1] == u:
p.r.high = self.ref[p.r.high]
if p.r.high is None and p.r.low is not None: # just emptied
self.ref[p.r.low] = p.l.low
self.side[p.r.low] = -1
p.r = Interval(high=p.r.high)
self.s.append(p)
def testTransposeTo(self):
for Ch, Int in self.TranspositionTest:
TransposedInterval = Interval(Ch[0][0],
Ch[0][1]).TransposeTo(Ch[1])
self.assertEqual(TransposedInterval.__repr__(), Int.__repr__())
print(Interval(Ch[0][0], Ch[0][1]), "transposed to ", Ch[1],
" gives", TransposedInterval)
def privStep(self, t):
self.node.setFluidPos(self._ProjectileInterval__calcPos(t))
Interval.privStep(self, t)
if self.collNode and self.collNode.getNumSolids() > 0:
csolid = self.collNode.modifySolid(0)
csolid.setT1(csolid.getT2())
csolid.setT2(t)
def privInstant(self):
self._ProjectileInterval__initialize()
Interval.privInstant(self)
if self.collNode:
self.collNode.clearSolids()
csolid = CollisionParabola(self.parabola, 0, self.duration)
self.collNode.addSolid(csolid)
def __init__(self,
particleEffect,
parent,
worldRelative=1,
renderParent=None,
duration=0.0,
softStopT=0.0,
cleanup=False,
name=None):
id = 'Particle-%d' % ParticleInterval.particleNum
ParticleInterval.particleNum += 1
if name == None:
name = id
self.particleEffect = particleEffect
self.cleanup = cleanup
if parent != None:
self.particleEffect.reparentTo(parent)
if worldRelative:
renderParent = render
if renderParent:
for particles in self.particleEffect.getParticlesList():
particles.setRenderParent(renderParent.node())
self.__softStopped = False
if softStopT == 0.0:
self.softStopT = duration
else:
if softStopT < 0.0:
self.softStopT = duration + softStopT
else:
self.softStopT = softStopT
Interval.__init__(self, name, duration)
return
def __init__(self,
particleEffect,
parent,
worldRelative = 1,
renderParent = None,
duration = 0.0,
softStopT = 0.0,
cleanup = False,
name = None):
"""
particleEffect is a ParticleEffect
parent is a NodePath: this is where the effect will be
parented in the scenegraph
worldRelative is a boolean: this will override 'renderParent'
with render
renderParent is a NodePath: this is where the particles will
be rendered in the scenegraph
duration is a float: for the time
softStopT is a float: no effect if 0.0,
a positive value will count from the
start of the interval,
a negative value will count from the
end of the interval
cleanup is a boolean: if True the effect will be destroyed
and removed from the scenegraph upon
interval completion
set to False if planning on reusing
the interval
name is a string: use this for unique intervals so that
they can be easily found in the taskMgr
"""
# Generate unique name
id = 'Particle-%d' % ParticleInterval.particleNum
ParticleInterval.particleNum += 1
if name == None:
name = id
# Record instance variables
self.particleEffect = particleEffect
self.cleanup = cleanup
if parent != None:
self.particleEffect.reparentTo(parent)
if worldRelative:
renderParent = render
if renderParent:
for particles in self.particleEffect.getParticlesList():
particles.setRenderParent(renderParent.node())
self.__softStopped = False
if softStopT == 0.0:
self.softStopT = duration
elif softStopT < 0.0:
self.softStopT = duration+softStopT
else:
self.softStopT = softStopT
# Initialize superclass
Interval.__init__(self, name, duration)
def __init__(self, left: Interval = None, right: Interval = None):
if left is None:
left = Interval()
if right is None:
right = Interval()
self.l = left
self.r = right
def __init__(self,
particleEffect,
duration=0.0,
parent = None,
renderParent = None,
name=None):
"""
particleEffect is ??
parent is ??
worldRelative is a boolean
loop is a boolean
duration is a float for the time
name is ??
"""
# Generate unique name
id = 'Particle-%d' % TestInterval.particleNum
TestInterval.particleNum += 1
if name == None:
name = id
# Record instance variables
self.particleEffect = particleEffect
self.parent = parent
self.renderParent = renderParent
Interval.__init__(self, name, duration)
def privInstant(self):
self.__initialize()
Interval.privInstant(self)
if self.collNode:
self.collNode.clearSolids()
csolid = CollisionParabola(self.parabola, 0, self.duration)
self.collNode.addSolid(csolid)
def __init__(
self,
node,
startPos=None,
endPos=None,
duration=None,
startVel=None,
endZ=None,
wayPoint=None,
timeToWayPoint=None,
gravityMult=None,
name=None,
):
"""
You may specify several different sets of input parameters.
(If startPos is not provided, it will be obtained from the node's
position at the time that the interval is first started. Note that
in this case you must provide a duration of some kind.)
# go from startPos to endPos in duration seconds
startPos, endPos, duration
# given a starting velocity, go for a specific time period
startPos, startVel, duration
# given a starting velocity, go until you hit a given Z plane
startPos, startVel, endZ
# pass through wayPoint at time 'timeToWayPoint'. Go until
# you hit a given Z plane
startPos, wayPoint, timeToWayPoint, endZ
You may alter gravity by providing a multiplier in 'gravityMult'.
'2.' will make gravity twice as strong, '.5' half as strong.
'-1.' will reverse gravity
"""
self.node = node
if name == None:
name = "%s-%s" % (self.__class__.__name__, self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
"""
# attempt to add info about the caller
file, line, func = PythonUtil.callerInfo()
if file is not None:
name += '-%s:%s:%s' % (file, line, func)
"""
args = (startPos, endPos, duration, startVel, endZ, wayPoint, timeToWayPoint, gravityMult)
self.implicitStartPos = 0
if startPos is None:
if duration is None:
self.notify.error("must provide either startPos or duration")
self.duration = duration
# we can't calc the trajectory until we know our starting
# position; delay until the interval is actually started
self.trajectoryArgs = args
self.implicitStartPos = 1
else:
self.__calcTrajectory(*args)
Interval.__init__(self, name, self.duration)
def __init__(self, node, startPos = None, endPos = None, duration = None, startVel = None, endZ = None, wayPoint = None, timeToWayPoint = None, gravityMult = None, name = None, collNode = None):
self.node = node
self.collNode = collNode
if self.collNode:
if isinstance(self.collNode, NodePath):
self.collNode = self.collNode.node()
if name == None:
name = '%s-%s' % (self.__class__.__name__, self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
args = (startPos,
endPos,
duration,
startVel,
endZ,
wayPoint,
timeToWayPoint,
gravityMult)
self.implicitStartPos = 0
if startPos is None:
if duration is None:
self.notify.error('must provide either startPos or duration')
self.duration = duration
self.trajectoryArgs = args
self.implicitStartPos = 1
else:
self.trajectoryArgs = args
self.__calcTrajectory(*args)
Interval.__init__(self, name, self.duration)
return
def privInitialize(self, t):
self.__initialize()
if self.collNode:
self.collNode.clearSolids()
csolid = CollisionParabola(self.parabola, 0, 0)
self.collNode.addSolid(csolid)
Interval.privInitialize(self, t)
def privStep(self, t):
self.node.setFluidPos(self.__calcPos(t))
Interval.privStep(self, t)
if self.collNode and self.collNode.getNumSolids() > 0:
csolid = self.collNode.modifySolid(0)
csolid.setT1(csolid.getT2())
csolid.setT2(t)
def get_octave(self):
octave = Interval(self.base_freq)
octave_freq = self.scale_intervals[0].final_frequency*2
octave.final_frequency = octave_freq
octave.note_number = self.NUM_INTERVALS
octave.set_note_name()
return octave
def __init__(self,
node,
startPos=None,
endPos=None,
duration=None,
startVel=None,
endZ=None,
wayPoint=None,
timeToWayPoint=None,
gravityMult=None,
name=None):
"""
You may specify several different sets of input parameters.
(If startPos is not provided, it will be obtained from the node's
position at the time that the interval is first started. Note that
in this case you must provide a duration of some kind.)
# go from startPos to endPos in duration seconds
startPos, endPos, duration
# given a starting velocity, go for a specific time period
startPos, startVel, duration
# given a starting velocity, go until you hit a given Z plane
startPos, startVel, endZ
# pass through wayPoint at time 'timeToWayPoint'. Go until
# you hit a given Z plane
startPos, wayPoint, timeToWayPoint, endZ
You may alter gravity by providing a multiplier in 'gravityMult'.
'2.' will make gravity twice as strong, '.5' half as strong.
'-1.' will reverse gravity
"""
self.node = node
if name == None:
name = '%s-%s' % (self.__class__.__name__,
self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
"""
# attempt to add info about the caller
file, line, func = PythonUtil.callerInfo()
if file is not None:
name += '-%s:%s:%s' % (file, line, func)
"""
args = (startPos, endPos, duration, startVel, endZ, wayPoint,
timeToWayPoint, gravityMult)
self.implicitStartPos = 0
if startPos is None:
if duration is None:
self.notify.error('must provide either startPos or duration')
self.duration = duration
# we can't calc the trajectory until we know our starting
# position; delay until the interval is actually started
self.trajectoryArgs = args
self.implicitStartPos = 1
else:
self.__calcTrajectory(*args)
Interval.__init__(self, name, self.duration)
def window_generator(self, chrom_length, window_size):
intervals = {}
for i in range(1, chrom_length + 1, window_size):
intervals[Interval(i, i + window_size - 1)] = []
if i + window_size - 1 < chrom_length + 1:
intervals[Interval(i + window_size, chrom_length)] = []
return intervals
def RecognizeInterval(self, Interval):
""" Gives a name to an interval """
NoteDistance = Interval.GetNoteNameDistance()
LookupValue = self.IntervalNameLookup[NoteDistance]
IName = LookupValue[0]
IntervalType = LookupValue[1]
Difference = Interval.GetDistance(
) - self.NominalHalfSteps[NoteDistance]
Modifier = self.Modifiers[IntervalType][Difference]
return IntervalName(IName, Modifier)
def privStep(self, t):
if self.state == CInterval.SPaused or t < self.currT:
self.privInitialize(t)
elif not (self._ParticleInterval__softStopped) and t > self.softStopT:
self._ParticleInterval__step(self.softStopT - self.currT)
self._ParticleInterval__softStop()
self._ParticleInterval__step(t - self.softStopT)
else:
self._ParticleInterval__step(t - self.currT)
Interval.privStep(self, t)
def privStep(self, t):
if self.state == CInterval.SPaused or t < self.currT:
self.privInitialize(t)
else:
if not self.__softStopped and t > self.softStopT:
self.__step(self.softStopT - self.currT)
self.__softStop()
self.__step(t - self.softStopT)
else:
self.__step(t - self.currT)
Interval.privStep(self, t)
def privInitialize(self, t):
if self.state != CInterval.SPaused:
self.__softStart()
if self.particleEffect:
self.particleEffect.clearToInitial()
self.currT = 0
if self.particleEffect:
for forceGroup in self.particleEffect.getForceGroupList():
forceGroup.enable()
Interval.privInitialize(self, t)
def __init__(self):
""" Interval knowledge consists of interval names and an interval type.
The interval name is a string (e.g. "third")
The interval type is either 1 or 2.
Intervals of type 1 can have modifiers: perfect, augmented, diminished, doubly augmented or doubly diminished.
Intervals of type 2 can have modifiers: major, minor, augmented, diminished, doubly augmented or doubly diminished.
"""
self.IntervalNameLookup = {
0: ["unison", 1],
1: ["second", 2],
2: ["third", 2],
3: ["fourth", 1],
4: ["fifth", 1],
5: ["sixth", 2],
6: ["seventh", 2],
7: ["octave", 1]
}
self.MajorScale = ['c', 'd', 'e', 'f', 'g', 'a', 'b']
self.ModifierKnowledgeType1 = {
-4: "quadruply diminished",
-3: "triply diminished",
-2: "doubly diminished",
-1: "diminished",
0: "perfect",
1: "augmented",
2: "doubly augmented",
3: "triply augmented",
4: "quadruply augmented"
}
self.ModifierKnowledgeType2 = {
-4: "triply diminished",
-3: "doubly diminished",
-2: "diminished",
-1: "minor",
0: "major",
1: "augmented",
2: "doubly augmented",
3: "triply augmented",
4: "quadruply augmented"
}
self.Modifiers = {
1: self.ModifierKnowledgeType1,
2: self.ModifierKnowledgeType2
}
self.NominalHalfSteps = {}
for Note in self.MajorScale:
self.NominalHalfSteps[Interval(
self.MajorScale[0], Note).GetNoteNameDistance()] = Interval(
self.MajorScale[0], Note).GetDistance()
def privInitialize(self, t):
if self.state != CInterval.SPaused:
self.__softStart()
if self.particleEffect:
self.particleEffect.clearToInitial()
self.currT = 0
if self.particleEffect:
for forceGroup in self.particleEffect.getForceGroupList():
forceGroup.enable()
Interval.privInitialize(self, t)
def privStep(self, t):
if self.state == CInterval.SPaused or t < self.currT:
# Restarting from a pause.
self.privInitialize(t)
else:
if not self.__softStopped and t > self.softStopT:
self.__step(self.softStopT - self.currT)
self.__softStop()
self.__step(t - self.softStopT)
else:
self.__step(t - self.currT)
Interval.privStep(self, t)
def loadTSS():
byGene={}
with open(TSS,"rt") as IN:
for line in IN:
fields=line.rstrip().split()
if(len(fields)!=4): continue
(chr,pos,strand,gene)=fields
pos=int(pos)
rec=Interval(pos,pos+1)
rec.chr=chr
byGene[gene]=rec
return byGene
def __init__(self, tipo):
assert type(tipo) == str, 'deve ser uma string'
if (tipo == 'Uniclass'):
self.restr = {'segmento': tipo, 'cartao': ['Básico'], 'plano_odonto': ['Básico'],
'limite_cred': Interval(1000, 4000)}
elif (tipo == 'Varejo'):
self.restr = {'segmento': tipo, 'cartao': ['Silver'], 'plano_odonto': ['Básico', 'Médio'],
'limite_cred': Interval(4000, 8000)}
else:
self.restr = {'segmento': tipo, 'cartao': ['Black', 'Platinum'], 'plano_odonto': ['Médio', 'Ouro'],
'limite_cred': Interval(8000, 50000)}
def getInterval(pos,exons):
numExons=len(exons)
for i in range(numExons):
exon=exons[i]
interval=None
if(pos+2==exon.getBegin()):
interval=Interval(exons[i-1].end,exon.getEnd())
elif(pos==exon.getEnd()):
interval=Interval(exon.getBegin(),exons[i+1].getBegin())
if(interval):
interval.exon=i
return interval
return None
def privStep(self, t):
if self.node:
if self.node.isEmpty():
self.pause()
return
else:
return
self.node.setFluidPos(self.__calcPos(t))
Interval.privStep(self, t)
if self.collNode and self.collNode.getNumSolids() > 0:
csolid = self.collNode.modifySolid(0)
csolid.setT1(csolid.getT2())
csolid.setT2(t)
class WebsiteMonitor:
def __init__(self, url, checkInterval):
self.url = url
self.checkInterval = checkInterval
# calculating the number of checks in an hour to initialize the history
maxNumberOfChecksSaved = int(round(3600.0 / checkInterval))
self.checksHistory = History(maxNumberOfChecksSaved)
# the history may be used by other threads, thus we protect it with a lock
self.historyLock = threading.Lock()
# interval keeps track of the Interval instance that execute self.check every self.checkInterval
self.interval = None
# keeps track of when the monitor was launched
self.startedMonitoringTime = time.time()
def check(self):
# HTTP HEAD request to the url of the monitored website
# measurez
success = True
checkTime = time.time()
try:
r = requests.head(self.url, timeout=min(self.checkInterval, 5.0))
except requests.exceptions.RequestException:
success = False
responseTime = time.time() - checkTime
with self.historyLock:
self.checksHistory.add((
-1 if not (success) else r.status_code,
checkTime,
-1.0 if not (success) else responseTime,
))
def startMonitoring(self):
self.startedMonitoringTime = time.time()
self.interval = Interval(self.checkInterval, self.check)
def stopMonitoring(self):
if self.interval != None:
self.interval.cancel()
self.interval = None
#####
# THREAD SAFE GETTER WITH CONDITION
#####
def getCheckHistoryForThePast(self, seconds):
t = time.time()
with self.historyLock:
# check[1] = timestamp of the check
return self.checksHistory.getValuesUntilCondition(
lambda check: t - check[1] > seconds)
def __init__(self, node, startPos = None, endPos = None, duration = None, startVel = None, endZ = None, gravityMult = None, name = None):
self.node = node
if name == None:
name = '%s-%s' % (self.__class__.__name__, self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
args = (startPos, endPos, duration, startVel, endZ, gravityMult)
self.needToCalcTraj = 0
if startPos is None:
self.trajectoryArgs = args
self.needToCalcTraj = 1
else:
self._ProjectileInterval__calcTrajectory(*args)
Interval.__init__(self, name, duration)
def loadHiC(expression):
seen=set()
with open(HIC,"rt") as IN:
for line in IN:
fields=line.rstrip().split()
(chr1,begin1,end1,chr2,begin2,end2)=fields
array=expression.get(chr1,None)
if(array is None): return
tad=Interval(int(begin1),int(end1))
tad.type="anchor"
tad.objects=[]
key=chr1+" "+begin1+" "+end1
if(key not in seen): array.append(tad)
seen.add(key)
def privInitialize(self, t):
if self.state != CInterval.SPaused:
# Restarting from a hard stop or just interrupting the
# current play
self.__softStart()
if self.particleEffect:
self.particleEffect.clearToInitial()
self.currT = 0
if self.particleEffect:
for forceGroup in self.particleEffect.getForceGroupList():
forceGroup.enable()
Interval.privInitialize(self,t)
def privInitialize(self, t):
if self.state != CInterval.SPaused:
# Restarting from a hard stop or just interrupting the
# current play
self.__softStart()
if self.particleEffect:
self.particleEffect.clearToInitial()
self.currT = 0
if self.particleEffect:
for forceGroup in self.particleEffect.getForceGroupList():
forceGroup.enable()
Interval.privInitialize(self, t)
def getRegionsAbove(self, cutoff):
"""getRegionsAbove() returns array of Intervals"""
data = self.data
if (self.isDiscrete()): raise Exception("track is not continuous")
L = len(data)
intervals = []
begin = None
for i in range(0, L):
x = data[i]
if (x > cutoff and (i == 0 or data[i - 1] <= cutoff)): begin = i
elif (x <= cutoff and i > 0 and data[i - 1] > cutoff):
intervals.append(Interval(begin, i))
if (L > 0 and data[L - 1] > cutoff):
intervals.append(Interval(begin, L))
return intervals
def getNonzeroRegions(self):
"""getNoneroRegions() returns array of Intervals"""
data = self.data
if (self.isDiscrete()): raise Exception("track is not continuous")
L = len(data)
intervals = []
begin = None
for i in range(0, L):
x = data[i]
if (x != 0 and (i == 0 or data[i - 1] == 0)): begin = i
elif (x == 0 and i > 0 and data[i - 1] != 0):
intervals.append(Interval(begin, i))
if (L > 0 and data[L - 1] != 0):
intervals.append(Interval(begin, L))
return intervals
def loop():
#initial input interval list
while True:
try:
int_list=input("List of intervals?")
if int_list.lower()=='quit':
sys.exit(0)
int_list=int_list.split(', ')
intervals=[]
for intv in int_list:
intervals.append(Interval(intv))
#break
intervals=mergeOverlapping(intervals)
except ValueError as message:
print(message)
except EOFError:
sys.exit(0)
def calculate_intervals(data):
begin = math.floor(get_minimum(data))
end = math.ceil(get_maximum(data))
count = round((end - begin) * 100 /
len(data)) # Calculation may be wrong for other data sets
step = round((end - begin) / count, 1)
intervals = [Interval() for i in range(count)]
current_border = begin
for interval in intervals:
interval.begin = round(current_border, 1)
interval.end = round(current_border + step, 1)
current_border += step
for value in data:
if value != end:
current_interval = intervals[int((value - begin) / step)]
else:
current_interval = intervals[count - 1]
current_interval.count += 1
current_interval.sum = round(current_interval.sum, 1) + value
for interval in intervals:
interval.probability = interval.count / (len(data) * step)
if interval.count != 0:
interval.mean = round(interval.sum / interval.count, 1)
return intervals
def computeIntervals(self, refPos):
ops = self.ops
n = len(ops)
begin1 = 0
begin2 = refPos
for i in range(n):
op = ops[i]
L = op.getLength()
end1 = begin1
end2 = begin2
if (op.advanceInQuery()): end1 += L
if (op.advanceInRef()): end2 += L
op.interval1 = Interval(begin1, end1)
op.interval2 = Interval(begin2, end2)
begin1 = end1
begin2 = end2
def getInterval(firstTd):
firstTd = firstTd.findAll(text=True)
for time in range(len(TimeLessonsBegin)):
if formatTime(firstTd[0]) == TimeLessonsBegin[time]:
interval = Interval(time + 1, formatTime(firstTd[0]),
formatTime(firstTd[1]))
return interval
return None
def conflicting(self, i: Interval, b: Tuple[str, str]) -> bool:
"""
Check conflicting edge against interval
@param i: Interval interval
@param b: Tuple[str, str] edge
@return: bool True when conflicting, otherwise False
"""
return not (i.empty()) and self.lowpt[i.high] > self.lowpt[b]
def getContiguousRegions(self):
"""getContiguousRegions() returns an array of Interval objects
with a "value" attribute added
"""
data=self.data
if(self.isDiscrete()): raise Exception("track is not continuous")
L=len(data)
intervals=[]
begin=0
for i in range(1,L):
x=data[i]
prev=data[i-1]
if(x==prev): continue
interval=Interval(begin,i)
interval.value=prev
intervals.append(interval)
begin=i
interval=Interval(begin,L)
interval.value=data[L-1]
intervals.append(interval)
return intervals
def insert(self, intervals, newInterval):
if len(intervals) == 0:
return [newInterval]
r = []
overlapWithNewInterval = Interval(newInterval.start, newInterval.end)
didAddNewInterval = False
for i in intervals:
if (i.start < overlapWithNewInterval.start
and i.end < overlapWithNewInterval.start):
r.append(i)
elif (i.start < overlapWithNewInterval.start
and i.end >= overlapWithNewInterval.start
and i.end <= overlapWithNewInterval.end):
overlapWithNewInterval.start = i.start
elif (i.start < overlapWithNewInterval.start
and i.end > overlapWithNewInterval.end):
return intervals
elif (i.start >= overlapWithNewInterval.start
and i.end <= overlapWithNewInterval.end):
pass
elif (i.start >= overlapWithNewInterval.start
and i.start <= overlapWithNewInterval.end
and i.end >= overlapWithNewInterval.end):
overlapWithNewInterval.end = i.end
else: # hxl: i is after overlapWithNewInterval
if didAddNewInterval == False:
r.append(overlapWithNewInterval)
didAddNewInterval = True
r.append(i)
# hxl: It's possible that the new interval is not added yet!
if didAddNewInterval == False:
r.append(overlapWithNewInterval)
didAddNewInterval = True
return r
def __init__(self, particleEffect, parent, worldRelative = 1, renderParent = None, duration = 0.0, softStopT = 0.0, cleanup = False, name = None):
id = 'Particle-%d' % ParticleInterval.particleNum
ParticleInterval.particleNum += 1
if name == None:
name = id
self.particleEffect = particleEffect
self.cleanup = cleanup
if parent != None:
self.particleEffect.reparentTo(parent)
if worldRelative:
renderParent = render
if renderParent:
for particles in self.particleEffect.getParticlesList():
particles.setRenderParent(renderParent.node())
self.__softStopped = False
if softStopT == 0.0:
self.softStopT = duration
elif softStopT < 0.0:
self.softStopT = duration + softStopT
else:
self.softStopT = softStopT
Interval.__init__(self, name, duration)
return
def privInstant(self):
self._ProjectileInterval__initialize()
Interval.privInstant(self)
def privInitialize(self, t):
self._ProjectileInterval__initialize()
Interval.privInitialize(self, t)
def parse(filehandle):
intervalstart = False
dimno = 0
for line in filehandle:
elems = [x.strip() for x in line.split('=')]
# Filter useless lines
if len(elems) < 2:
continue
if not intervalstart:
if elems[0] == 'Object class':
objectclass = elems[1]
elif elems[0] == 'xmin':
xmin = float(elems[1])
elif elems[0] == 'xmax':
xmax = float(elems[1])
elif elems[0] == 'nx':
size = int(elems[1])
elif elems[0] == 'dx':
shift = float(elems[1])
elif elems[0] == 'x1':
start = float(elems[1])
elif elems[0] == 'maximumNumberOfCoefficients':
dimensions = float(elems[1]) + 1
intervalstart = True
# Increase size to hold first Interval object as padding
mfccTier = Tier(xmin, xmax, size+1, objectclass)
mfccTier.shift = shift
text = np.zeros(dimensions)
first = Interval(0.0, start, text)
mfccTier.addInterval(first)
continue
elif intervalstart:
if elems[0] == 'c0':
dimno = 0
vec = np.zeros(dimensions)
vec[dimno] = float(elems[1])
elif elems[0] == 'numberOfCoefficients':
assert int(elems[1]) <= dimensions
elif elems[0][0] == 'c':
dimno += 1
#print(dimno)
vec[dimno] = float(elems[1])
#print(vec)
if dimensions == dimno+1:
#print('here, ...')
begin = mfccTier[-1].xmax
end = begin + mfccTier.shift
interval = Interval(begin, end, vec)
interval.viewable = False
mfccTier.addInterval(interval)
return mfccTier
#!/usr/bin/python
from Interval import Interval
import random
#
# Simple code for testing the Interval module, and showing how it is used
#
interval = Interval(1.5, 2.5)
for i in range(1, 100):
interval.add(random.random() * 10)
print interval.getCount()
interval.clear()
print interval.getCount()
def privFinalize(self):
Interval.privFinalize(self)
if self.cleanup and self.particleEffect:
self.particleEffect.cleanup()
self.particleEffect = None
def main():
usage = "usage: %prog [options] chromInfo.bed"
parser = OptionParser(usage)
parser.add_option("--morgan", type="float", dest="morgan", default=100000000, help="physical length of 1 Morgan (default 100Mbp)")
parser.add_option("--grandpaternaltwobit", type="string", dest="paternaltbf", help="2bit file representing (grand)paternal haplotype")
parser.add_option("--grandmaternaltwobit", type="string", dest="maternaltbf", help="2bit file representing (grand)maternal haplotype")
parser.add_option("--samplename", type="string", dest="samplename", help="sample name for which you are generating a gamete for", default="gamete")
parser.add_option("--meiosis", type="int", dest="nmeiosis", help="meiotic event id (default 1) ", default=1)
parser.add_option("--chromSize", type="int", dest="chromSize", help="length of chromosome", default=1000000)
parser.add_option("--theta", type="float", dest='theta', help='crossover rate', default=0)
(options, args)=parser.parse_args()
if options.maternaltbf == None:
#pass
sys.stderr.write("please provide maternal 2bit file!\n")
exit(1)
if options.paternaltbf == None:
#pass
sys.stderr.write("please provide paternal 2bit file!\n")
exit(1)
paternalname = str.split ( os.path.basename(options.paternaltbf) , '.')[0]
maternalname = str.split ( os.path.basename(options.maternaltbf) , '.')[0]
print paternalname, maternalname
try:
sys.stderr.write("opening paternal twobitfile...\n")
twobit_paternal=bx.seq.twobit.TwoBitFile( open( options.paternaltbf ) )
except:
sys.stderr.write("unable to open paternal twobit file!\n")
try:
sys.stderr.write("opening maternal twobitfile...\n")
twobit_maternal=bx.seq.twobit.TwoBitFile( open( options.maternaltbf ) )
except:
sys.stderr.write("unable to open maternal twobit file!\n")
crossoverfh=open("sample."+options.samplename+".meiosis_"+str(options.nmeiosis)+".crossover.log", 'w')
chromSizes=[]
if options.theta == 0:
lambdaval= float(options.chromSize)/float(options.morgan)
else:
lambdaval=options.theta
sys.stderr.write("generating crossover intervals ...\n")
gametesequence=[]
chrom='1'
crossoverfh.write("lambda value: " + str(lambdaval) + "\n")
#get the number of crossovers by drawing from poisson
n=np.random.poisson(lambdaval, 1)
ncrossovers=n[0]
#pick haplotype to pass
flip=np.random.uniform(0,1)
if flip <= .5:
haplotype="maternal"
else:
haplotype="paternal"
intervalstring=''
#now get the crossover points and record them in Interval format http://107.20.183.198/documentation.php#interval-format
#if zero crossovers, then just past the entire chromosome
if ncrossovers ==0:
intervalstring="\t".join([haplotype, chrom, "+",'0', str(options.chromSize), str(ncrossovers),',',','])
crossoverfh.write(chrom + " " + haplotype + " " + str(ncrossovers) + " " + str(options.chromSize) + "\n")
#otherise randomly throw down crossover points according to uniform random
else:
chromsize=options.chromSize
points=np.random.random_integers(1, chromsize, ncrossovers)
points.sort()
pointstrings=[]
for p in points: pointstrings.append(str(p))
outstring="\t".join(pointstrings)
crossoverfh.write(chrom + " " + haplotype + " " + str(ncrossovers) + " " + ",".join(pointstrings) + "\n")
if len(points) %2 == 0:
#sys.stderr.write(haplotype + " " + chrom + " " + outstring +"\n")
starts=list(points[1::2])
ends=list(points[::2])
ends.append(int(chromsize))
starts.insert(0,0)
startstrings=",".join(map(lambda x: str(x), starts))
endstrings=",".join(map(lambda x: str(x), ends))
intervalstring="\t".join([haplotype, chrom, "+",str(starts[0]), str(ends[-1]),str(ncrossovers), startstrings, endstrings])
else:
#sys.stderr.write(haplotype + " " + chrom + " " + outstring +"\n")
starts=list(points[1::2])
ends=list(points[0::2])
starts.insert(0,0)
startstrings=",".join(map(lambda x: str(x), starts))
endstrings=",".join(map(lambda x: str(x), ends))
#print starts
#print ends
intervalstring="\t".join([haplotype, chrom, "+",str(starts[0]), str(ends[-1]),str(ncrossovers), startstrings, endstrings])
#print intervalstring
print intervalstring
intervalobj=Interval(intervalstring)
if haplotype=='maternal':
inbtwn_name='paternal'
else:
inbtwn_name='maternal'
print intervalstring
#extract DNA sequence from the maternal/paternal 2bit files according to the crossover intervals
for (bedstring) in intervalobj.toBedstring():
crossoverfh.write(bedstring+"\n")
if haplotype=='maternal':
(chr, start, end, name)=bedstring.split('\t')
chr=maternalname
bedstring="\t".join([ chr, start,end,name])
print bedstring
gametesequence += twoBitExtract(bedstring, twobit_maternal)
else:
(chr, start, end, name)=bedstring.split('\t')
chr=paternalname
bedstring="\t".join([ chr, start,end,name])
print bedstring
gametesequence += twoBitExtract(bedstring, twobit_paternal)
#print "=="
for bedstring in intervalobj.yieldInBtwnBedstring(inbtwn_name):
crossoverfh.write(bedstring+"\n")
if inbtwn_name=='maternal':
(chr, start, end, name)=bedstring.split('\t')
chr=maternalname
bedstring="\t".join([ chr, start,end,name])
gametesequence += twoBitExtract(bedstring, twobit_maternal)
else:
(chr, start, end, name)=bedstring.split('\t')
chr=paternalname
bedstring="\t".join([ chr, start,end,name])
gametesequence += twoBitExtract(bedstring, twobit_paternal)
if intervalobj.getLastSubIntervalEnd() != -1 and intervalobj.getLastSubIntervalEnd() < chromsize:
#print inbtwn_name, chrom, intervalobj.getLastSubIntervalEnd(), chromsize
bedstring="\t".join(map( lambda(x): str(x), [ chrom, intervalobj.getLastSubIntervalEnd(), chromsize, inbtwn_name ] ) )
crossoverfh.write(bedstring+"\n")
if inbtwn_name=='maternal':
(chr, start, end, name)=bedstring.split('\t')
chr=maternalname
bedstring="\t".join([ chr, start,end,name])
gametesequence += twoBitExtract(bedstring, twobit_maternal)
else:
(chr, start, end, name)=bedstring.split('\t')
chr=paternalname
bedstring="\t".join([ chr, start,end,name])
gametesequence += twoBitExtract(bedstring, twobit_paternal)
#finally write out teh fasta file
sys.stderr.write("writing gametic fasta file ... " + chrom + "\n")
gametefastaname="_".join([chrom,"gamete", "meiosis"+str(options.nmeiosis), options.samplename])
#writefasta("".join(gametesequence), chrom + "." + options.samplename, gametefastaname+".fa")
writefasta("".join(gametesequence),options.samplename, options.samplename+".fa")
def start(self,*args,**kwargs):
self.particleEffect.clearToInitial()
self.currT = 0
Interval.start(self,*args,**kwargs)
def privStep(self, t):
self.node.setPos(self._ProjectileInterval__calcPos(t))
Interval.privStep(self, t)
def testTransposeTo(self):
for Ch, Int in self.TranspositionTest:
TransposedInterval = Interval(Ch[0][0],Ch[0][1]).TransposeTo(Ch[1])
self.assertEqual(TransposedInterval.__repr__(), Int.__repr__())
print Interval(Ch[0][0],Ch[0][1]),"transposed to ",Ch[1]," gives",TransposedInterval
else:
begin=exons[exonIndex-1].getEnd()
pos=exon.getBegin()-2
end=exon.getEnd()
else:
if(siteType=="donor"):
begin=exons[exonIndex-1].getEnd()
pos=exon.getBegin()-2
end=exon.getEnd()
else:
begin=exon.getBegin()
pos=exon.getEnd()
end=exons[exonIndex+1].getBegin()
exclusions=exclude.get(substrate,{})
begin=int(begin); pos=int(pos); end=int(end)
interval=Interval(pos-70,pos+70)
if(interval.begin<begin): interval.begin=begin
if(interval.end>end): interval.end=end
juncs=junctions.get(substrate,[])
#print("substrate=",substrate)
sum=0
for junc in juncs:
(substrate,begin,end,count)=junc
key=str(begin)+"-"+str(end)
if(exclusions.get(key,False)):
continue
if(interval.contains(begin) or interval.contains(end)): sum+=int(count)
geneCount=readCounts.get(geneID,0)
#print("gene=",geneID)
if(rex.find("(\S+)_\d",geneID)): geneID=rex[1]
print(indiv,hap,geneID,transID,strand,exonIndex,siteType,interval.begin,pos,
def privInitialize(self, t):
self.__initialize()
Interval.privInitialize(self, t)
def privInstant(self):
self.__initialize()
Interval.privInstant(self)
def privStep(self, t):
self.node.setFluidPos(self.__calcPos(t))
Interval.privStep(self, t)
def __init__(self, node, startPos = None,
endPos = None, duration = None,
startVel = None, endZ = None,
wayPoint = None, timeToWayPoint = None,
gravityMult = None, name = None,
collNode = None):
"""
You may specify several different sets of input parameters.
(If startPos is not provided, it will be obtained from the node's
position at the time that the interval is first started. Note that
in this case you must provide a duration of some kind.)
# go from startPos to endPos in duration seconds
startPos, endPos, duration
# given a starting velocity, go for a specific time period
startPos, startVel, duration
# given a starting velocity, go until you hit a given Z plane
startPos, startVel, endZ
# pass through wayPoint at time 'timeToWayPoint'. Go until
# you hit a given Z plane
startPos, wayPoint, timeToWayPoint, endZ
You may alter gravity by providing a multiplier in 'gravityMult'.
'2.' will make gravity twice as strong, '.5' half as strong.
'-1.' will reverse gravity
If collNode is not None, it should be an empty CollisionNode
which will be filled with an appropriate CollisionParabola
when the interval starts. This CollisionParabola will be set
to match the interval's parabola, and its t1, t2 values will
be updated automatically as the interval plays. It will *not*
be automatically removed from the node when the interval
finishes.
"""
self.node = node
self.collNode = collNode
if self.collNode:
if isinstance(self.collNode, NodePath):
self.collNode = self.collNode.node()
assert self.collNode.getNumSolids() == 0
if name == None:
name = '%s-%s' % (self.__class__.__name__,
self.projectileIntervalNum)
ProjectileInterval.projectileIntervalNum += 1
args = (startPos, endPos, duration, startVel, endZ,
wayPoint, timeToWayPoint, gravityMult)
self.implicitStartPos = 0
if startPos is None:
if duration is None:
self.notify.error('must provide either startPos or duration')
self.duration = duration
# we can't calc the trajectory until we know our starting
# position; delay until the interval is actually started
self.trajectoryArgs = args
self.implicitStartPos = 1
else:
self.trajectoryArgs = args
self.__calcTrajectory(*args)
Interval.__init__(self, name, self.duration)