RNA Project 2021_10

from matplotlib import pyplot as plt
import math
import re
import heapq
from scipy.spatial.distance import hamming
import statistics

f = open("/Users/rafiqkamal/Desktop/Data_Science/RNAProject210110/RNAL20StructuresGSSizes.txt")
contents = f.readlines()

frequencyStructureArray = []
histogramArray = []

for line in contents:
    x = re.findall("\d+",line)
    y = re.findall("[()\.]+",line)
    frequencyStructureArray.append([int(x[0]),y[0]])
    histogramArray.append(math.log10(int(x[0])))
frequencyStructureArray.sort()

plt.figure("RNA Histogram")
plt.hist(histogramArray,bins = 5, ec="black")
plt.xlabel("log10 of Frequencies")
plt.ylabel("Number of Occurences")

threeLargest = heapq.nlargest(3,frequencyStructureArray)
threeSmallest = heapq.nsmallest(3,frequencyStructureArray)

print("The three largest frequencies are" , threeLargest)
print("The three smallest frequencies are " , threeSmallest)

theLargest = threeLargest[0]
theSmallest = threeSmallest[0]
theSecondLargest = threeLargest[1]
theThirdLargest = threeLargest[2]
theSecondSmallest = threeSmallest[1]
theThirdSmallest = threeSmallest[2]

highestFreqHammingDistances = []
smallestFreqHammingDistances = []
secondLargestFreqHammingDistances = []
thirdLargestFreqHammingDistances = []
secondSmallestFreqHammingDistances = []
thirdSmallestFreqHammingDistances = []

for line in frequencyStructureArray:
    lineArray = list(line[1])
    largestArray = list(theLargest[1])
    smallestArray = list(theSmallest[1])
    secondLargestArray = list(theSecondLargest[1])
    thirdLargestArray = list(theThirdLargest[1])
    secondSmallestArray = list(theSecondSmallest[1])
    thirdSmallestArray = list(theThirdSmallest[1])
    highestFreqHammingDistances.append(hamming(lineArray,largestArray) * len(lineArray))
    smallestFreqHammingDistances.append(hamming(lineArray,smallestArray) * len(lineArray))
    secondLargestFreqHammingDistances.append(hamming(lineArray,secondLargestArray) * len(lineArray))
    thirdLargestFreqHammingDistances.append(hamming(lineArray,thirdLargestArray) * len(lineArray))
    secondSmallestFreqHammingDistances.append(hamming(lineArray,secondSmallestArray) * len(lineArray))
    thirdSmallestFreqHammingDistances.append(hamming(lineArray, thirdSmallestArray) * len(lineArray))

highestFreqHammingDistances.sort()
smallestFreqHammingDistances.sort()
secondLargestFreqHammingDistances.sort()
thirdLargestFreqHammingDistances.sort()
secondSmallestFreqHammingDistances.sort()
thirdSmallestFreqHammingDistances.sort()

plt.figure("Highest Frequencies Histogram")
plt.hist(highestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Highest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.figure("Second Highest Frequencies Histogram")
plt.hist(secondLargestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Second Highest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.figure("Third Highest Frequencies Histogram")
plt.hist(thirdLargestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Third Highest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.figure("Lowest Frequencies Histogram")
plt.hist(smallestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Lowest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.figure("Second Lowest Frequencies Histogram")
plt.hist(secondSmallestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Second Lowest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.figure("Third Lowest Frequencies Histogram")
plt.hist(thirdLargestFreqHammingDistances,bins = 5, ec="black")
plt.xlabel("Third Lowest Frequencies Histogram")
plt.ylabel("Number of Occurences")

plt.show()

meanOfHighestFreqHammingDistances = statistics.mean(highestFreqHammingDistances)
meanOfSecondHighestFreqHammingDistances = statistics.mean(secondLargestFreqHammingDistances)
meanOfThirdHighestFreqHammingDistances = statistics.mean(thirdLargestFreqHammingDistances)
meanOfSmallestFreqHammingDistances = statistics.mean(smallestFreqHammingDistances)
meanOfSecondSmallestFreqHammingDistances = statistics.mean(secondSmallestFreqHammingDistances)
meanOfThirdSmallestFreqHammingDistances = statistics.mean(thirdSmallestFreqHammingDistances)

print("The mean of the highest frequencies Hamming distance is " + str(round(meanOfHighestFreqHammingDistances,2)))

print("The mean of the second highest frequencies Hamming distance is " + str(round(meanOfSecondHighestFreqHammingDistances,2)))
print("The mean of the third highest frequencies Hamming distance is " + str(round(meanOfThirdHighestFreqHammingDistances,2)))

print("The mean of the smallest frequencies Hamming distance is " + str(round(meanOfSmallestFreqHammingDistances,2)))
print("The mean of the second smallest frequencies Hamming distance is " + str(round(meanOfSecondSmallestFreqHammingDistances,2)))
print("The mean of the third smallest frequencies Hamming distance is " + str(round(meanOfThirdSmallestFreqHammingDistances,2)))