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NanoporeClasses.py
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Sun, May 5, 06:55

NanoporeClasses.py
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import numpy as np
from pprint import pprint
import shelve
import os
import math
from Plotting.NanoporePlots import PlotCurrentTrace,PlotCurrentTraceBaseline
class TranslocationEvent:
def __init__(self, filename):
self.filename = filename
def SetEvent(self,eventTrace,baseline,samplerate):
self.eventTrace=eventTrace
self.baseline=baseline
self.samplerate=samplerate
self.meanTrace=np.mean(eventTrace)
self.lengthEvents=len(eventTrace)/samplerate
self.currentDrop=baseline-np.mean(eventTrace)
def SetCoefficients(self,coefficients):
self.coefficients=coefficients
def SetBaselineTrace(self, before,after):
self.before=before
self.after=after
def PlotEvent(self):
part1=np.append(self.before,self.eventTrace)
currentTrace=np.append(part1,self.after)
#PlotCurrentTrace(currentTrace,self.samplerate)
PlotCurrentTraceBaseline(self.before,self.eventTrace,self.after,self.samplerate)
class AllEvents:
def __init__(self):
self.events=[]
def AddEvent(self, translocationEvent):
if isinstance(translocationEvent,AllEvents):
self.events.extend(translocationEvent.events)
elif isinstance(translocationEvent,list):
self.events.extend(translocationEvent)
else:
self.events.append(translocationEvent)
def GetAllLengths(self):
Lengths=[event.lengthEvents for event in self.events]
return Lengths
def GetAllIdrops(self):
currentDrops=[event.currentDrop for event in self.events]
return currentDrops
def SaveEvents(self,folder):
savefile=os.path.join(folder,os.path.basename(folder)+'_Events')
shelfFile=shelve.open(savefile)
shelfFile['TranslocationEvents']=self.events
shelfFile.close()
print('saved as: ' + savefile)
def GetEventsMinCondition(self,minCurrent=-math.inf,maxCurrent=math.inf,minLength=0,maxLength=math.inf):
minCurrent = -math.inf if not minCurrent else minCurrent
maxCurrent = math.inf if not maxCurrent else maxCurrent
minLength = 0 if not minLength else minLength
maxLength = math.inf if not maxLength else maxLength
newEvents=AllEvents()
for event in self.events:
if minCurrent<event.currentDrop<maxCurrent and minLength<event.lengthEvents<maxLength:
newEvents.AddEvent(event)
print('selected {} events from {}'.format(len(newEvents.events), len(self.events)))
return newEvents
def PlotAllEvents(self):
for event in self.events:
event.PlotEvent()

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