Plotting Lists in Python

Question

I'm trying to make a Plot of two lists, once shall have the time measured with timeit and the other the amount of times i ran through the loop. I only get an empty plot so i figured that something is wrong. Could somebody perhaps tell me where the mistake is? The functions are not really important but I will post the whole thing to provide context. Here is the code:

import random
import timeit
import matplotlib.pyplot as plt

def generateSequences(n):

    RandomSequences = []
    dna = ["A","G","C","T"]
    for i in range(int(n)):

        randseq=''

        for i in range(50):
            randseq+=random.choice(dna)

        RandomSequences.append(randseq)

    return RandomSequences

def generatePrefixes(p, RandomSequences):

    First20Chars = [x[:20] for x in RandomSequences]
    RandomChoices = []
    for i in range(p):
        randomPrefix = random.choice(First20Chars)
        RandomChoices.append(randomPrefix)

    return First20Chars, RandomChoices

def searchReadsInList(RandomSequences, RandomChoices):

    start_time = timeit.default_timer()
    Matches_RS_RC = []
    for i in RandomChoices:
        for j in RandomSequences:
            if i in j:
                Matches_RS_RC.append(j)
    elapsed_sRL = timeit.default_timer() - start_time
    return Matches_RS_RC, elapsed_sRL



if __name__ == "__main__":
    count = 10
    while count < 1000:
        RandomSequences = generateSequences(count)
        First20Chars, RandomChoices = generatePrefixes(5, RandomSequences)
        Matches_RS_RC, elapsed_sRL = searchReadsInList(RandomSequences, RandomChoices)
        ListCounts = []
        ListCounts.append(count)
        ListTime = []
        ListTime.append(elapsed_sRL)
        count = count + 10

    plt.plot(ListTime, count)
    plt.xlabel('Time')
    plt.ylabel('# of Reads')
    plt.savefig("TimePlot.pdf")
    plt.show()

Your lists store only 2 values: [990] and [0.0012807846069335938]. When plot use plt.plot(ListTime, ListCounts). — Serenity
– Serenity, Commented Jun 1, 2016 at 9:17

Serenity · Accepted Answer · 2016-06-01 09:19:28Z

1

I improve the main function, you had cleared lists on an every iteration:

if __name__ == "__main__":
    count = 10
    ListCounts = []
    ListTime = []

    while count < 1000:
        RandomSequences = generateSequences(count)
        First20Chars, RandomChoices = generatePrefixes(5, RandomSequences)
        Matches_RS_RC, elapsed_sRL = searchReadsInList(RandomSequences, RandomChoices)
        ListCounts.append(count)
        ListTime.append(elapsed_sRL)
        count = count + 10

    print ListCounts
    print ListTime

    plt.plot(ListTime, ListCounts)
    plt.xlabel('Time')
    plt.ylabel('# of Reads')
    plt.savefig("TimePlot.pdf")
    plt.show()

answered Jun 1, 2016 at 9:19

Serenity

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